Effect of a Protein Supplement on the Gut Microbiota of Endurance Athletes: A Randomized, Controlled, Double-Blind Pilot Study
Nutritional supplements are popular among athletes to improve performance and physical recovery. Protein supplements fulfill this function by improving performance and increasing muscle mass; however, their effect on other organs or systems is less well known. Diet alterations can induce gut microbiota imbalance, with beneficial or deleterious consequences for the host. To test this, we performed a randomized pilot study in cross-country runners whose diets were complemented with a protein supplement (whey isolate and beef hydrolysate) (n = 12) or maltodextrin (control) (n = 12) for 10 weeks. Microbiota, water content, pH, ammonia, and short-chain fatty acids (SCFAs) were analyzed in fecal samples, whereas malondialdehyde levels (oxidative stress marker) were determined in plasma and urine. Fecal pH, water content, ammonia, and SCFA concentrations did not change, indicating that protein supplementation did not increase the presence of these fermentation-derived metabolites. Similarly, it had no impact on plasma or urine malondialdehyde levels; however, it increased the abundance of the Bacteroidetes phylum and decreased the presence of health-related taxa including Roseburia, Blautia, and Bifidobacterium longum. Thus, long-term protein supplementation may have a negative impact on gut microbiota. Further research is needed to establish the impact of protein supplements on gut microbiota.
Improving the UNC Passive Aerosol Sampler Model Based on Comparison with Commonly Used Aerosol Sampling Methods
AbstractObjectivesIn an occupational environment, passive sampling could be an alternative to active sampling with pumps for sampling of dust. One passive sampler is the University of North Carolina passive aerosol sampler (UNC sampler). It is often analysed by microscopic imaging. Promising results have been shown for particles above 2.5 µm, but indicate large underestimations for PM2.5. The aim of this study was to evaluate, and possibly improve, the UNC sampler for stationary sampling in a working environment.MethodsSampling was carried out at 8-h intervals during 24 h in four locations in an open pit mine with UNC samplers, respirable cyclones, PM10 and PM2.5 impactors, and an aerodynamic particle sizer (APS). The wind was minimal. For quantification, two modifications of the UNC sampler analysis model, UNC sampler with hybrid model and UNC sampler with area factor, were compared with the original one, UNC sampler with mesh factor derived from wind tunnel experiments. The effect of increased resolution for the microscopic imaging was examined.ResultsUse of the area factor and a higher resolution eliminated the underestimation for PM10 and PM2.5. The model with area factor had the overall lowest deviation versus the impactor and the cyclone. The intraclass correlation (ICC) showed that the UNC sampler had a higher precision and better ability to distinguish between different exposure levels compared to the cyclone (ICC: 0.51 versus 0.24), but lower precision compared to the impactor (PM10: 0.79 versus 0.99; PM2.5: 0.30 versus 0.45). The particle size distributions as calculated from the different UNC sampler analysis models were visually compared with the distributions determined by APS. The distributions were obviously different when the UNC sampler with mesh factor was used but came to a reasonable agreement when the area factor was used.ConclusionsHigh resolution combined with a factor based on area only, results in no underestimation of small particles compared to impactors and cyclones and a better agreement with the APS’s particle size distributions. The UNC sampler had lower precision than the impactors, but higher than the respirable cyclone. The UNC sampler with area factor could be used for PM2.5, PM10 and respirable fraction measurements in this working environment without wind.
Unexpected binding behaviors of bacterial Argonautes in human cells cast doubts on their use as targetable gene regulators
Prokaryotic Argonaute proteins (pAgos) have been proposed as an alternative to the CRISPR/Cas9 platform for gene editing. Although Argonaute from Natronobacterium gregoryi (NgAgo) was recently shown unable to cleave genomic DNA in mammalian cells, the utility of NgAgo or other pAgos as a targetable DNA-binding platform for epigenetic editing has not been explored. In this report, we evaluated the utility of two prokaryotic Argonautes (NgAgo and TtAgo) as DNA-guided DNA-binding proteins. NgAgo showed no meaningful binding to chromosomal targets, while TtAgo displayed seemingly non-specific binding to chromosomal DNA even in the absence of guide DNA. The observed lack of DNA-guided targeting and unexpected guide-independent genome sampling under the conditions in this study provide evidence that these pAgos might be suitable for neither gene nor epigenome editing in mammalian cells.
Preterm Infant Feeding: A Mechanistic Comparison between a Vacuum Triggered Novel Teat and Breastfeeding
The goal for preterm infants is to achieve full oral feeds quickly and ultimately progress to full breastfeeding. Supplementary oral feeds are often given when the mother is not available to breastfeed. Bottles typically deliver milk in a different fashion compared to breastfeeding, which is thought to hamper transition to full breastfeeding. The aim of this study was to compare the sucking dynamics of preterm infants fed at the breast to feeding with an experimental novel teat (NT) designed to release milk only upon the application of vacuum. Simultaneous ultrasound imaging of the infant oral cavity and measurement of intra-oral vacuum was performed during a breastfeed and a feed with the NT. Test weighs were used to measure milk intake. Linear mixed effects models were performed to investigate differences by feed type, and simultaneous linear regression was performed to investigate individual patterns. Tongue movement was not different between breastfeeding and the NT. Intra-oral vacuums (median (interquartile range: IQR)) were significantly lower with the NT (Baseline vacuum: −5.8 mmHg (−11.0, 0.1); Peak: 40.0 mmHg (−54.6, −27.1)) compared to breastfeeding (Baseline: −31.1 mmHg (−60.0, −12.7); Peak: −106.2 mmHg (−153.0, −65.5)). Milk intake was significantly higher with the NT (33 mL (22.5, 42.5)) compared to the breastfeed (12 mL (3, 15.5)). The novel teat encouraged a similar tongue action to breastfeeding, and infants transferred a greater volume of milk with the novel teat. Intra-oral vacuums were lower in strength with the novel teat compared to the breast. Use of the novel teat for the training of sucking dynamics in preterm infants has the potential to improve breastfeeding success and requires further investigation.
Analysis of Transposable Elements in Coccidioides Species
Coccidioides immitis and C. posadasii are primary pathogenic fungi that cause disease in immunologically-normal animals and people. The organism is found exclusively in arid regions of the Southwestern United States, Mexico, and South America, but not in other parts of the world. This study is a detailed analysis of the transposable elements (TE) in Coccidioides spp. As is common in most fungi, Class I and Class II transposons were identified and the LTR Gypsy superfamily is the most common. The minority of Coccidioides Gypsy transposons contained regions highly homologous to polyprotein domains. Phylogenetic analysis of the integrase and reverse transcriptase sequences revealed that many, but not all, of the Gypsy reverse transcriptase and integrase domains clustered by species suggesting extensive transposition after speciation of the two Coccidiodies spp. The TEs were clustered and the distribution is enriched for the ends on contigs. Analysis of gene expression data from C. immitis found that protein-coding genes within 1 kB of hAT or Gypsy TEs were poorly expressed. The expression of C. posadasii genes within 1 kB of Gypsy TEs was also significantly lower compared to all genes but the difference in expression was smaller than C. immitis. C. posadasii orthologs of C. immitis Gyspsy-associated genes were also likely to be TE-associated. In both C. immitis and C. posadasii the TEs were preferentially associated with genes annotated with protein kinase gene ontology terms. These observations suggest that TE may play a role in influencing gene expression in Coccidioides spp. Our hope is that these bioinformatic studies of the potential TE influence on expression and evolution of Coccidioides will prompt the development of testable hypotheses to better understand the role of TEs in the biology and gene regulation of Coccidioides spp.
Impact of Prolonged Blood Incubation and Extended Serum Storage at Room Temperature on the Human Serum Metabolome
Metabolomics is a powerful technology with broad applications in life science that, like other -omics approaches, requires high-quality samples to achieve reliable results and ensure reproducibility. Therefore, along with quality assurance, methods to assess sample quality regarding pre-analytical confounders are urgently needed. In this study, we analyzed the response of the human serum metabolome to pre-analytical variations comprising prolonged blood incubation and extended serum storage at room temperature by using gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) -based metabolomics. We found that the prolonged incubation of blood results in a statistically significant 20% increase and 4% decrease of 225 tested serum metabolites. Extended serum storage affected 21% of the analyzed metabolites (14% increased, 7% decreased). Amino acids and nucleobases showed the highest percentage of changed metabolites in both confounding conditions, whereas lipids were remarkably stable. Interestingly, the amounts of taurine and O-phosphoethanolamine, which have both been discussed as biomarkers for various diseases, were 1.8- and 2.9-fold increased after 6 h of blood incubation. Since we found that both are more stable in ethylenediaminetetraacetic acid (EDTA) blood, EDTA plasma should be the preferred metabolomics matrix.
Using human brain activity to guide machine learning
Machine learning is a field of computer science that builds algorithms that learn. In many cases, machine learning algorithms are used to recreate a human ability like adding a caption to a photo, driving a car, or playing a game. While the human brain has long served as a source of inspiration for machine learning, little effort has been made to directly use data collected from working brains as a guide for machine learning algorithms. Here we demonstrate a new paradigm of “neurally-weighted” machine learning, which takes fMRI measurements of human brain activity from subjects viewing images, and infuses these data into the training process of an object recognition learning algorithm to make it more consistent with the human brain. After training, these neurally-weighted classifiers are able to classify images without requiring any additional neural data. We show that our neural-weighting approach can lead to large performance gains when used with traditional machine vision features, as well as to significant improvements with already high-performing convolutional neural network features. The effectiveness of this approach points to a path forward for a new class of hybrid machine learning algorithms which take both inspiration and direct constraints from neuronal data.
Sponges-Cyanobacteria associations: Global diversity overview and new data from the Eastern Mediterranean
Sponge-cyanobacteria associations have attracted research interest from an ecological, evolutionary and biotechnological perspective. Current knowledge is, in its majority, “hidden” in metagenomics research studying the entire microbial communities of sponges, while knowledge on these associations is totally missing for certain geographic areas. In this study, we (a) investigated the occurrence of cyanobacteria in 18 sponge species, several of which are studied for the first time for their cyanobionts, from a previously unexplored eastern Mediterranean ecoregion, the Aegean Sea, (b) isolated sponge-associated cyanobacteria, and characterized them based on a polyphasic (morphological-morphometric and molecular phylogenetic analysis) approach, and (c) conducted a meta-analysis on the global diversity of sponge species hosting cyanobacteria, as well as the diversity of cyanobacterial symbionts. Our research provided new records for nine sponge species, previously unknown for this association, while the isolated cyanobacteria were found to form novel clades within Synechococcus, Leptolyngbyaceae, Pseudanabaenaceae, and Schizotrichaceae, whose taxonomic status requires further investigation; this is the first report of a Schizotrichaceae cyanobacterium associated with sponges. The extensive evaluation of the literature along with the new data from the Aegean Sea raised the number of sponge species known for hosting cyanobacteria to 320 and showed that the cyanobacterial diversity reported from sponges is yet underestimated.
High-resolution GPS tracking reveals sex differences in migratory behaviour and stopover habitat use in the Lesser Black-backed Gull Larus fuscus
Sex-, size- or age-dependent variation in migration strategies in birds is generally expected to reflect differences in competitive abilities. Theoretical and empirical studies thereby focus on differences in wintering areas, by which individuals may benefit from avoiding food competition during winter or ensuring an early return and access to prime nesting sites in spring. Here, we use GPS tracking to assess sex- and size-related variation in the spatial behaviour of adult Lesser Black-backed Gulls (Larus fuscus) throughout their annual cycle. We did not find sex- or size-dependent differences in wintering area or the timing of spring migration. Instead, sexual differences occurred prior to, and during, autumn migration, when females strongly focussed on agricultural areas. Females exhibited a more protracted autumn migration strategy, hence spent more time on stopover sites and arrived 15 days later at their wintering areas, than males. This shift in habitat use and protracted autumn migration coincided with the timing of moult, which overlaps with chick rearing and migration. Our results suggest that this overlap between energy-demanding activities may lead females to perform a more prolonged autumn migration, which results in spatiotemporal differences in foraging habitat use between the sexes.
A π-Halogen Bond of Dibenzofuranones with the Gatekeeper Phe113 in Human Protein Kinase CK2 Leads to Potent Tight Binding Inhibitors
Human protein kinase CK2 is an emerging target for neoplastic diseases. Potent lead structures for human CK2 inhibitors are derived from dibenzofuranones. Two new derivatives, 7,9-dichloro-1,2-dihydro-8-hydroxy-4-[(4-methoxyphenylamino)-methylene]dibenzo[b,d]furan-3(2H)-one (4a) and (E)-1,3-dichloro-6-[(4-methoxyphenylimino)-methyl]dibenzo[b,d]furan-2,7-diol (5) were tested for inhibition of CK2 and induction of apoptosis in LNCaP cells. Both turned out to be tight binding inhibitors, with IC50 values of 7 nM (4a) and 5 nM (5) and an apparent Ki value of 0.4 nM for both. Compounds 4a and 5 reduced cellular CK2 activity, indicating cell permeability. Cell viability was substantially impaired in LNCaP cells, as well as apoptosis was induced, which was not appearing in non-neoplastic ARPE-19 cells. Co-crystallization of 4a and 5 revealed an unexpected π-halogen bond of the chloro substituent at C9 with the gatekeeper amino acid Phe113, leading to an inverted binding mode in comparison to parent compound 4b, with the Cl at C6 instead, which was co-crystallized as a control. This indicates that the position of the chloro substituent on ring A of the dibenzofuran scaffold is responsible for an inversion of the binding mode that enhances potency.
SYK expression level distinguishes control from BRCA1-mutated lymphocytes
BackgroundAbout 5%–10% of breast cancer and 10%–15% of ovarian cancer are hereditary. BRCA1 and BRCA2 are the most common germline mutations found in both inherited breast and ovarian cancers. Once these mutations are identified and classified, a course of action to reduce the risk of developing either ovarian or breast cancer – including surveillance and surgery – is carried out.PurposeThe purpose of the current research is to characterize the gene expression differences between healthy cells harboring a mutation in BRCA1/2 genes and normal cells. This will allow detection of candidate genes and help identify women who carry functional BRCA1/2 mutations, which cannot always be detected by the available sequencing methods, for example, carriers of mutations found in regulatory sequences of the genes.Materials and methodsOur cohort consisted of 50 healthy women, of whom 24 were individuals with BRCA1 or BRCA2 heterozygous mutations and 26 were non-carrier controls. RNA purified from non-irradiated lymphocytes of nine BRCA1/2 mutation carriers versus four control mutation-negative individuals was utilized for RNA-Seq analysis. The selected RNA-Seq transcripts were validated, and the levels of spleen tyrosine kinase (SYK) mRNA were measured by using real-time quantitative polymerase chain reaction.ResultsDifferences in gene expression were found when comparing untreated lymphocytes of BRCA1/2 mutation carriers and controls. Among others, the SYK gene was identified as being differently expressed for BRCA1/2 mutation carriers. The expression level of SYK was significantly higher in untreated healthy lymphocytes of BRCA1 heterozygote carriers compared with controls, regardless of irradiation. In contrast to normal tissues, in cancerous breast tissues, the expression levels of the BRCA1 and SYK genes were not intercorrelated.ConclusionCollectively, our observations demonstrate that SYK may prove to be a good candidate for better diagnosis, treatment, and prevention of BRCA1 mutation-associated breast cancer.
Combined classification system based on ACR/EULAR and ultrasonographic scores for improving the diagnosis of Sjögren's syndrome
We retrospectively evaluated the effectiveness of combined use of salivary gland ultrasonography (US) and the 2016 American College of Rheumatology/European League Against Rheumatic Disease (ACR/EULAR) classification criteria for improving the diagnostic efficiency in patients with Sjögren’s syndrome (SS). A US-based salivary gland disease grading system was developed using a cohort comprising 213 SS or non-SS patients who fulfilled the minimum requirements for classifying SS based on the American-European Consensus Group (AECG) and ACR criteria. Using 62 SS or non-SS patients from the 213 patients and who had also undergone all the 5 examinations needed for the ACR/EULAR classification, we compared the diagnostic accuracy of various combinations of the ACR/EULAR and US classifications for diagnosing SS, using the clinical diagnosis of SS by rheumatologists as the gold standard. The ACR/EULAR criteria discriminated clinical SS patients with 77% and 79% accuracy for those with primary or secondary SS and for those with primary SS, respectively. However, the integrated score system of the ACR/EULAR and US classifications yielded 92% and 93% accuracy for these 2 SS patient groups, respectively, provided that US score of 3 was assigned to patients with US grade ≥2, and then patients with integrated threshold score of ≥5 were diagnosed as SS. Cross-validation also indicated improved accuracy of the integrated ACR/EULAR and US score system (91.9 and 93.0% for primary/secondary and primary SS patients, respectively) over that by the ACR/EULAR criteria alone. (74.2 and 86.0%, respectively). The integrated ACR/EULAR and US scoring system can improve the diagnosis of patients with clinical SS.
Long-term effects of stimulant exposure on cerebral blood flow response to methylphenidate and behavior in attention-deficit hyperactivity disorder
Stimulant prescription rates for attention deficit hyperactivity disorder (ADHD) are increasing, even though potential long-term effects on the developing brain have not been well-studied. A previous randomized clinical trial showed short-term age-dependent effects of stimulants on the DA system. We here assessed the long-term modifying effects of age-of-first-stimulant treatment on the human brain and behavior. 81 male adult ADHD patients were stratified into three groups: 1) early stimulant treatment (EST; <16 years of age) 2) late stimulant treatment (LST: ≥23 years of age) and 3) stimulant treatment naive (STN; no history of stimulant treatment). We used pharmacological magnetic resonance imaging (phMRI) to assess the cerebral blood flow (CBF) response to an oral methylphenidate challenge (MPH, 0.5 mg/kg), as an indirect measure of dopamine function in fronto-striatal areas. In addition, mood and anxiety scores, and recreational drug use were assessed. Baseline ACC CBF was lower in the EST than the STN group (p = 0.03), although CBF response to MPH was similar between the three groups (p = 0.23). ADHD symptom severity was higher in the STN group compared to the other groups (p < 0.01). In addition, the EST group reported more depressive symptoms (p = 0.04), but not anxiety (p = 0.26), and less recreational drug use (p = 0.04). In line with extensive pre-clinical data, our data suggest that early, but not late, stimulant treatment long-lastingly affects the human brain and behavior, possibly indicating fundamental changes in the dopamine system.
A Transcriptomic Analysis of Xylan Mutants Does Not Support the Existence of a Secondary Cell Wall Integrity System in Arabidopsis
Yeast have long been known to possess a cell wall integrity (CWI) system, and recently an analogous system has been described for the primary walls of plants (PCWI) that leads to changes in plant growth and cell wall composition. A similar system has been proposed to exist for secondary cell walls (SCWI). However, there is little data to support this. Here, we analyzed the stem transcriptome of a set of cell wall biosynthetic mutants in order to investigate whether cell wall damage, in this case caused by aberrant xylan synthesis, activates a signaling cascade or changes in cell wall synthesis gene expression. Our data revealed remarkably few changes to the transcriptome. We hypothesize that this is because cells undergoing secondary cell wall thickening have entered a committed programme leading to cell death, and therefore a SCWI system would have limited impact. The absence of transcriptomic responses to secondary cell wall alterations may facilitate engineering of the secondary cell wall of plants.
A Bayesian Semiparametric Regression Model for Joint Analysis of Microbiome Data
The successional dynamics of microbial communities are influenced by the synergistic interactions of physical and biological factors. In our motivating data, ocean microbiome samples were collected from the Santa Cruz Municipal Wharf, Monterey Bay at multiple time points and then 16S ribosomal RNA (rRNA) sequenced. We develop a Bayesian semiparametric regression model to investigate how microbial abundance and succession change with covarying physical and biological factors including algal bloom and domoic acid concentration level using 16S rRNA sequencing data. A generalized linear regression model is built using the Laplace prior, a sparse inducing prior, to improve estimation of covariate effects on mean abundances of microbial species represented by operational taxonomic units (OTUs). A nonparametric prior model is used to facilitate borrowing strength across OTUs, across samples and across time points. It flexibly estimates baseline mean abundances of OTUs and provides the basis for improved quantification of covariate effects. The proposed method does not require prior normalization of OTU counts to adjust differences in sample total counts. Instead, the normalization and estimation of covariate effects on OTU abundance are simultaneously carried out for joint analysis of all OTUs. Using simulation studies and a real data analysis, we demonstrate improved inference compared to an existing method.
RNA-Seq analysis validates the use of culture-derived Trypanosoma brucei and provides new markers for mammalian and insect life-cycle stages
BackgroundTrypanosoma brucei brucei, the parasite causing Nagana in domestic animals, is closely related to the parasites causing sleeping sickness, but does not infect humans. In addition to its importance as a pathogen, the relative ease of genetic manipulation and an innate capacity for RNAi extend its use as a model organism in cell and infection biology. During its development in its mammalian and insect (tsetse fly) hosts, T. b. brucei passes through several different life-cycle stages. There are currently four life-cycle stages that can be cultured: slender forms and stumpy forms, which are equivalent to forms found in the mammal, and early and late procyclic forms, which are equivalent to forms in the tsetse midgut. Early procyclic forms show coordinated group movement (social motility) on semi-solid surfaces, whereas late procyclic forms do not.ResultsRNA-Seq was performed on biological replicates of each life-cycle stage. These constitute the first datasets for culture-derived slender and stumpy bloodstream forms and early and late procyclic forms. Expression profiles confirmed that genes known to be stage-regulated in the animal and insect hosts were also regulated in culture. Sequence reads of 100–125 bases provided sufficient precision to uncover differential expression of closely related genes. More than 100 transcripts showed peak expression in stumpy forms, including adenylate cyclases and several components of inositol metabolism. Early and late procyclic forms showed differential expression of 73 transcripts, a number of which encoded proteins that were previously shown to be stage-regulated. Moreover, two adenylate cyclases previously shown to reduce social motility are up-regulated in late procyclic forms.ConclusionsThis study validates the use of cultured bloodstream forms as alternatives to animal-derived parasites and yields new markers for all four stages. In addition to underpinning recent findings that early and late procyclic forms are distinct life-cycle stages, it could provide insights into the reasons for their different biological properties.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4600-6) contains supplementary material, which is available to authorized users.
Single Session Low Frequency Left Dorsolateral Prefrontal Transcranial Magnetic Stimulation Changes Neurometabolite Relationships in Healthy Humans
Background: Dorsolateral prefrontal cortex (DLPFC) low frequency repetitive transcranial magnetic stimulation (LF-rTMS) has shown promise as a treatment and investigative tool in the medical and research communities. Researchers have made significant progress elucidating DLPFC LF-rTMS effects—primarily in individuals with psychiatric disorders. However, more efforts investigating underlying molecular changes and establishing links to functional and behavioral outcomes in healthy humans are needed.Objective: We aimed to quantify neuromolecular changes and relate these to functional changes following a single session of DLPFC LF-rTMS in healthy participants.Methods: Eleven participants received sham-controlled neuronavigated 1 Hz rTMS to the region most activated by a 7-letter Sternberg working memory task (SWMT) within the left DLPFC. We quantified SWMT performance, functional magnetic resonance activation and proton Magnetic resonance spectroscopy (MRS) neurometabolite measure changes before and after stimulation.Results: A single LF-rTMS session was not sufficient to change DLPFC neurometabolite levels and these changes did not correlate with DLPFC activation changes. Real rTMS, however, significantly altered neurometabolite correlations (compared to sham rTMS), both with baseline levels and between the metabolites themselves. Additionally, real rTMS was associated with diminished reaction time (RT) performance improvements and increased activation within the motor, somatosensory and lateral occipital cortices.Conclusion: These results show that a single session of LF-rTMS is sufficient to influence metabolite relationships and causes widespread activation in healthy humans. Investigating correlational relationships may provide insight into mechanisms underlying LF-rTMS.
Impaired coordination of nucleophile and increased hydrophobicity in the +1 subsite shift levansucrase activity towards transfructosylation
AbstractBacterial levansucrases produce β(2,6)-linked levan-type polysaccharides using sucrose or sucrose analogs as donor/acceptor substrates. However, the dominant reaction of Bacillus megaterium levansucrase (Bm-LS) is hydrolysis. Single domain levansucrases from Gram-positive bacteria display a wide substrate-binding pocket with open access to water, challenging engineering for transfructosylation-efficient enzymes. We pursued a shift in reaction specificity by either modifying the water distribution in the active site or the coordination of the catalytic acid/base (E352) and the nucleophile (D95), thus affecting the fructosyl-transfer rate and allowing acceptors other than water to occupy the active site. Two serine (173/422) and two water-binding tyrosine (421/439) residues located in the first shell of the catalytic pocket were modified. Library variants of S173, Y421 and S422, which coordinate the position of D95 and E352, show increased transfructosylation (30–200%) and modified product spectra. Substitutions at position 422 have a higher impact on sucrose affinity, while changes at position 173 and 421 have a strong effect on the overall catalytic rate. As most retaining glycoside hydrolases (GHs) Bm-LS catalyzes hydrolysis and transglycosylation via a double displacement reaction involving two-transition states (TS1 and TS2). Hydrogen bonds of D95 with the side chains of S173 and S422 contribute a total of 2.4 kcal mol−1 to TS1 stabilization, while hydrogen bonds between invariant Y421, E352 and the glucosyl C-2 hydroxyl-group of sucrose contribute 2.15 kcal mol−1 stabilization. Changes at Y439 render predominantly hydrolytic variants synthesizing shorter oligosaccharides.
Probing the nature of gold–carbon bonding in gold–alkynyl complexes
Homogeneous catalysis by gold involves organogold complexes as precatalysts andreaction intermediates. Fundamental knowledge of the gold–carbon bonding iscritical to understanding the catalytic mechanisms. However, limited spectroscopicinformation is available about organogolds that are relevant to gold catalysts. Herewe report an investigation of the gold–carbon bonding ingold(I)–alkynyl complexes using photoelectron spectroscopy and theoreticalcalculations. We find that the gold–carbon bond in theClAu–CCH− complex represents one of the strongestgold–ligand bonds—even stronger than the known gold–carbonmultiple bonds, revealing an inverse correlation between bond strength and bondorder. The gold–carbon bond in LAuCCH− is found todepend on the ancillary ligands and becomes stronger for more electronegativeligands. The strong gold–carbon bond underlies the catalytic aptness of goldcomplexes for the facile formation of terminal alkynyl–gold intermediates andactivation of the carbon–carbon triple bond.
Neural retina-specific Aldh1a1 controls dorsal choroidal vascular development via Sox9 expression in retinal pigment epithelial cells
VEGF secreted from retinal pigment epithelial (RPE) cells is responsible for the choroidal vascular development; however, the molecular regulatory mechanism is unclear. We found that Aldh1a1–/– mice showed choroidal hypoplasia with insufficient vascularization in the dorsal region, although Aldh1a1, an enzyme that synthesizes retinoic acids (RAs), is expressed in the dorsal neural retina, not in the RPE/choroid complex. The level of VEGF in the RPE/choroid was significantly decreased in Aldh1a1–/– mice, and RA-dependent enhancement of VEGF was observed in primary RPE cells. An RA-deficient diet resulted in dorsal choroidal hypoplasia, and simple RA treatment of Aldh1a1–/– pregnant females suppressed choroid hypoplasia in their offspring. We also found downregulation of Sox9 in the dorsal neural retina and RPE of Aldh1a1–/– mice and RPE-specific disruption of Sox9 phenocopied Aldh1a1–/– choroidal development. These results suggest that RAs produced by Aldh1a1 in the neural retina directs dorsal choroidal vascular development via Sox9 upregulation in the dorsal RPE cells to enhance RPE-derived VEGF secretion.
Interrupted breeding in a songbird migrant triggers development of nocturnal locomotor activity
Long-distance avian migrants, e.g. Eurasian reed warblers (Acrocephalus scirpaceus), can precisely schedule events of their annual cycle. However, the proximate mechanisms controlling annual cycle and their interplay with environmental factors are poorly understood. We artificially interrupted breeding in reed warblers by bringing them into captivity and recording birds’ locomotor activity for 5–7 days. Over this time, most of the captive birds gradually developed nocturnal locomotor activity not observed in breeding birds. When the birds were later released and radio-tracked, the individuals with highly developed caged activity performed nocturnal flights. We also found that reed warblers kept indoors without access to local cues developed a higher level of nocturnal activity compared to the birds kept outdoors with an access to the familiar environment. Also, birds translocated from a distant site (21 km) had a higher motivation to fly at night-time after release compared to the birds captured within 1 km of a study site. Our study suggests that an interrupted breeding triggers development of nocturnal locomotor activity in cages, and the level of activity is correlated with motivation to perform nocturnal flights in the wild, which can be restrained by familiar environment.
Uncovering the Mechanisms of Chinese Herbal Medicine (MaZiRenWan) for Functional Constipation by Focused Network Pharmacology Approach
MaZiRenWan (MZRW, also known as Hemp Seed Pill) is a Chinese Herbal Medicine which has been demonstrated to safely and effectively alleviate functional constipation (FC) in a randomized, placebo-controlled clinical study with 120 subjects. However, the underlying pharmacological actions of MZRW for FC, are still largely unknown. We systematically analyzed the bioactive compounds of MZRW and mechanism-of-action biological targets through a novel approach called “focused network pharmacology.” Among the 97 compounds identified by UPLC-QTOF-MS/MS in MZRW extract, 34 were found in rat plasma, while 10 were found in rat feces. Hierarchical clustering analysis suggest that these compounds can be classified into component groups, in which compounds are highly similar to each other and most of them are from the same herb. Emodin, amygdalin, albiflorin, honokiol, and naringin were selected as representative compounds of corresponding component groups. All of them were shown to induce spontaneous contractions of rat colonic smooth muscle in vitro. Network analysis revealed that biological targets in acetylcholine-, estrogen-, prostaglandin-, cannabinoid-, and purine signaling pathways are able to explain the prokinetic effects of representative compounds and corresponding component groups. In conclusion, MZRW active components enhance colonic motility, possibly by acting on multiple targets and pathways.
Computed tomography diagnosed cachexia and sarcopenia in 725 oncology patients: is nutritional screening capturing hidden malnutrition?
AbstractBackgroundNutrition screening on admission to hospital is mandated in many countries, but to date, there is no consensus on which tool is optimal in the oncology setting. Wasting conditions such as cancer cachexia (CC) and sarcopenia are common in cancer patients and negatively impact on outcomes; however, they are often masked by excessive adiposity. This study aimed to inform the application of screening in cancer populations by investigating whether commonly used nutritional screening tools are adequately capturing nutritionally vulnerable patients, including those with abnormal body composition phenotypes (CC, sarcopenia, and myosteatosis).MethodsA prospective study of ambulatory oncology outpatients presenting for chemotherapy was performed. A detailed survey incorporating clinical, nutritional, biochemical, and quality of life data was administered. Participants were screened for malnutrition using the Malnutrition Universal Screening Tool (MUST), Malnutrition Screening Tool (MST), and the Nutritional Risk Index (NRI). Computed tomography (CT) assessment of body composition was performed to diagnose CC, sarcopenia, and myosteatosis according to consensus criteria.ResultsA total of 725 patients (60% male, median age 64 years) with solid tumours participated (45% metastatic disease). The majority were overweight/obese (57%). However, 67% were losing weight, and CT analysis revealed CC in 42%, sarcopenia in 41%, and myosteatosis in 46%. Among patients with CT‐identified CC, the MUST, MST, and NRI tools categorized 27%, 35%, and 7% of them as ‘low nutritional risk’, respectively. The percentage of patients with CT‐identified sarcopenia and myosteatosis that were categorised as ‘low nutritional risk’ by MUST, MST and NRI were 55%, 61%, and 14% and 52%, 50%, and 11%, respectively. Among these tools, the NRI was most sensitive, with scores <97.5 detecting 85.8%, 88.6%, and 92.9% of sarcopenia, myosteatosis, and CC cases, respectively. Using multivariate Cox proportional hazards models, NRI score < 97.5 predicted greater mortality risk (hazard ratio 1.8, confidence interval: 1.2–2.8, P = 0.007).ConclusionsHigh numbers of nutritionally vulnerable patients, with demonstrated abnormal body composition phenotypes on CT analysis, were misclassified by MUST and MST. Caution should be exercised when categorizing the nutritional risk of oncology patients using these tools. NRI detected the majority of abnormal body composition phenotypes and independently predicted survival. Of the tools examined, the NRI yielded the most valuable information from screening and demonstrated usefulness as an initial nutritional risk grading system in ambulatory oncology patients.
Characterization of thiol‐based redox modifications of Brassica napusSNF1‐related protein kinase 2.6‐2C
Sucrose nonfermenting 1‐related protein kinase 2.6 (SnRK2.6), also known as Open Stomata 1 (OST1) in Arabidopsis thaliana, plays a pivotal role in abscisic acid (ABA)‐mediated stomatal closure. Four SnRK2.6 paralogs were identified in the Brassica napus genome in our previous work. Here we studied one of the paralogs, BnSnRK2.6‐2C, which was transcriptionally induced by ABA in guard cells. Recombinant BnSnRK2.6‐2C exhibited autophosphorylation activity and its phosphorylation sites were mapped. The autophosphorylation activity was inhibited by S‐nitrosoglutathione (GSNO) and by oxidized glutathione (GSSG), and the inhibition was reversed by reductants. Using monobromobimane (mBBr) labeling, we demonstrated a dose‐dependent modification of BnSnRK2.6‐2C by GSNO. Furthermore, mass spectrometry analysis revealed previously uncharacterized thiol‐based modifications including glutathionylation and sulfonic acid formation. Of the six cysteine residues in BnSnRK2.6‐2C, C159 was found to have different types of thiol modifications, suggesting its high redox sensitivity and versatility. In addition, mBBr labeling on tyrosine residues was identified. Collectively, these data provide detailed biochemical characterization of redox‐induced modifications and changes of the BnSnRK2.6‐2C activity.
Heel impact forces during barefoot versus minimally shod walking among Tarahumara subsistence farmers and urban Americans
Despite substantial recent interest in walking barefoot and in minimal footwear, little is known about potential differences in walking biomechanics when unshod versus minimally shod. To test the hypothesis that heel impact forces are similar during barefoot and minimally shod walking, we analysed ground reaction forces recorded in both conditions with a pedography platform among indigenous subsistence farmers, the Tarahumara of Mexico, who habitually wear minimal sandals, as well as among urban Americans wearing commercially available minimal sandals. Among both the Tarahumara (n = 35) and Americans (n = 30), impact peaks generated in sandals had significantly (p < 0.05) higher force magnitudes, slower loading rates and larger vertical impulses than during barefoot walking. These kinetic differences were partly due to individuals' significantly greater effective mass when walking in sandals. Our results indicate that, in general, people tread more lightly when walking barefoot than in minimal footwear. Further research is needed to test if the variations in impact peaks generated by walking barefoot or in minimal shoes have consequences for musculoskeletal health.
A multi-step transcriptional cascade underlies vascular regeneration in vivo
The molecular mechanisms underlying vascular regeneration and repair are largely unknown. To gain insight into this process, we developed a method of intima denudation, characterized the progression of endothelial healing, and performed transcriptome analysis over time. Next-generation RNA sequencing (RNAseq) provided a quantitative and unbiased gene expression profile during in vivo regeneration following denudation injury. Our data indicate that shortly after injury, cells immediately adjacent to the wound mount a robust and rapid response with upregulation of genes like Jun, Fos, Myc, as well as cell adhesion genes. This was quickly followed by a wave of proliferative genes. After completion of endothelial healing a vigorous array of extracellular matrix transcripts were upregulated. Gene ontology enrichment and protein network analysis were used to identify transcriptional profiles over time. Further data mining revealed four distinct stages of regeneration: shock, proliferation, acclimation, and maturation. The transcriptional signature of those stages provides insight into the regenerative machinery responsible for arterial repair under normal physiologic conditions.
Molecular Mechanisms Underlying Curcumin-Mediated Therapeutic Effects in Type 2 Diabetes and Cancer
The growing prevalence of age-related diseases, especially type 2 diabetes mellitus (T2DM) and cancer, has become global health and economic problems. Due to multifactorial nature of both diseases, their pathophysiology is not completely understood so far. Compelling evidence indicates that increased oxidative stress, resulting from an imbalance between production of reactive oxygen species (ROS) and their clearance by antioxidant defense mechanisms, as well as the proinflammatory state contributes to the development and progression of the diseases. Curcumin (CUR; diferuloylmethane), a well-known polyphenol derived from the rhizomes of turmeric Curcuma longa, has attracted a great deal of attention as a natural compound with beneficial antidiabetic and anticancer properties, partly due to its antioxidative and anti-inflammatory actions. Although this polyphenolic compound is increasingly being recognized for its growing number of protective health effects, the precise molecular mechanisms through which it reduces diabetes- and cancer-related pathological events have not been fully unraveled. Hence, CUR is the subject of intensive research in the fields Diabetology and Oncology as a potential candidate in the treatment of both T2DM and cancer, particularly since current therapeutic options for their treatment are not satisfactory in clinics. In this review, we summarize the recent progress made on the molecular targets and pathways involved in antidiabetic and anticancer activities of CUR that are responsible for its beneficial health effects.
Adaptive differentiation of Festuca rubra along a climate gradient revealed by molecular markers and quantitative traits
Species response to climate change is influenced by predictable (selective) and unpredictable (random) evolutionary processes. To understand how climate change will affect present-day species, it is necessary to assess their adaptive potential and distinguish it from the effects of random processes. This will allow predicting how different genotypes will respond to forecasted environmental change. Space for time substitution experiments are an elegant way to test the response of present day populations to climate variation in real time. Here we assess neutral and putatively adaptive variation in 11 populations of Festuca rubra situated along crossed gradients of temperature and moisture using molecular markers and phenotypic measurements, respectively. By comparing population differentiation in putatively neutral molecular markers and phenotypic traits (QST-FST comparisons), we show the existence of adaptive differentiation in phenotypic traits and their plasticity across the climatic gradient. The observed patterns of differentiation are due to the high genotypic and phenotypic differentiation of the populations from the coldest (and wettest) environment. Finally, we observe statistically significant covariation between markers and phenotypic traits, which is likely caused by isolation by adaptation. These results contribute to a better understanding of the current adaptation and evolutionary potential to face climate change of a widespread species. They can also be extrapolated to understand how the studied populations will adjust to upcoming climate change without going through the lengthy process of phenotyping.
Age is reflected in the Fractal Dimensionality of MRI Diffusion Based Tractography
Fractal analysis is a widely used tool to analyze the geometrical complexity of biological structures. The geometry of natural objects such as plants, clouds, cellular structures, blood vessel, and many others cannot be described sufficiently with Euclidian geometric properties, but can be represented by a parameter called the fractal dimension. Here we show that a specific estimate of fractal dimension, the correlation dimension, is able to describe changes in the structural complexity of the human brain, based on data from magnetic resonance diffusion imaging. White matter nerve fiber bundles, represented by tractograms, were analyzed with regards to geometrical complexity, using fractal geometry. The well-known age-related change of white matter tissue was used to verify changes by means of fractal dimension. Structural changes in the brain were successfully be observed and quantified by fractal dimension and compared with changes in fractional anisotropy.
Selective Labeling of Individual Neurons in Dense Cultured Networks With Nanoparticle-Enhanced Photoporation
Neurodevelopmental and neurodegenerative disorders are characterized by subtle alterations in synaptic connections and perturbed neuronal network functionality. A hallmark of neuronal connectivity is the presence of dendritic spines, micron-sized protrusions of the dendritic shaft that compartmentalize single synapses to fine-tune synaptic strength. However, accurate quantification of spine density and morphology in mature neuronal networks is hampered by the lack of targeted labeling strategies. To resolve this, we have optimized a method to deliver cell-impermeable compounds into selected cells based on Spatially resolved NAnoparticle-enhanced Photoporation (SNAP). We show that SNAP enables efficient labeling of selected individual neurons and their spines in dense cultured networks without affecting short-term viability. We compare SNAP with widely used spine labeling techniques such as the application of lipophilic dyes and genetically encoded fluorescent markers. Using SNAP, we demonstrate a time-dependent increase in spine density in healthy cultures as well as a reduction in spine density after chemical mimicry of hypoxia. Since the sparse labeling procedure can be automated using an intelligent acquisition scheme, SNAP holds promise for high-content screening campaigns of neuronal connectivity in the context of neurodevelopmental and neurodegenerative disorders.
Phylogenomics and barcoding of Panax: toward the identification of ginseng species
BackgroundThe economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination.ResultsWe used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on a 163 kbp matrix resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species P. vietnamensis is supported as sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus.ConclusionsMBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and it provides an incentive for manufacturers to create authentic products with verified ingredients.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1160-y) contains supplementary material, which is available to authorized users.
Identification of a nicotinamide/nicotinate mononucleotide adenylyltransferase in Giardia lamblia (GlNMNAT)
Giardia lamblia is an intestinal protozoan parasite that causes giardiasis, a disease of high prevalence in Latin America, Asia and Africa. Giardiasis leads to poor absorption of nutrients, severe electrolyte loss and growth retardation. In addition to its clinical importance, this parasite is of special biological interest due to its basal evolutionary position and simplified metabolism, which has not been studied thoroughly. One of the most important and conserved metabolic pathways is the biosynthesis of nicotinamide adenine dinucleotide (NAD). This molecule is widely known as a coenzyme in multiple redox reactions and as a substrate in cellular processes such as synthesis of Ca2+ mobilizing agents, DNA repair and gene expression regulation. There are two pathways for NAD biosynthesis, which converge at the step catalyzed by nicotinamide/nicotinate mononucleotide adenylyltransferase (NMNAT, EC Using bioinformatics tools, we found two NMNAT sequences in Giardia lamblia (glnmnat-a and glnmnat-b). We first verified the identity of the sequences in silico. Subsequently, glnmnat-a was cloned into an expression vector. The recombinant protein (His-GlNMNAT) was purified by nickel-affinity binding and was used in direct in vitro enzyme assays assessed by C18-HPLC, verifying adenylyltransferase activity with both nicotinamide (NMN) and nicotinic acid (NAMN) mononucleotides. Optimal reaction pH and temperature were 7.3 and 26 °C. Michaelis–Menten kinetics were observed for NMN and ATP, but saturation was not accomplished with NAMN, implying low affinity yet detectable activity with this substrate. Double-reciprocal plots showed no cooperativity for this enzyme. This represents an advance in the study of NAD metabolism in Giardia spp.
PCR-RFLP assay as an option for primary HPV test
Persistent human papillomavirus (HPV) infection is an essential factor of cervical cancer. This study evaluated the analytical performance of restriction fragment length polymorphism polymerase chain reaction (PCR-RFLP) assay compared to PapilloCheck® microarray to identify human papilloma virus (HPV) in cervical cells. Three hundred and twenty-five women were analyzed. One sample was used for conventional cytology and another sample was collected using BD SurePath™ kit for HPV tests. Eighty samples (24.6%) were positive for HPV gene by PCR-Multiplex and were then submitted to PCR-RFLP and PapilloCheck® microarray. There was a genotyping agreement in 71.25% (57/80) on at least one HPV type between PCR-RFLP and PapilloCheck® microarray. In 22 samples (27.5%), the results were discordant and those samples were additionally analyzed by DNA sequencing. HPV 16 was the most prevalent HPV type found in both methods, followed by HPVs 53, 68, 18, 39, and 66 using PCR-RFLP analysis, and HPVs 39, 53, 68, 56, 31, and 66 using PapilloCheck® microarray. In the present study, a perfect agreement using Cohen's kappa (κ) was found in HPV 33 and 58 (κ=1), very good for HPV 51, and good for types 16, 18, 53, 59, 66, 68, 70, and 73. PCR-RFLP analysis identified only 25% (20/80) HPV coinfection, and PapilloCheck® microarray found 62.5% (50/80). Our Cohen's kappa results indicate that our in-house HPV genotyping testing (PCR-RFLP analysis) could be applied as a primary HPV test screening, especially in low income countries. If multiple HPV types are found in this primary test, a more descriptive test, such as PapilloCheck® microarray, could be performed.
The relationships between brain structural changes and perceived loneliness in older adults suffering from late‐life depression
ObjectiveLate‐life depression is a significant health risk factor for older adults, part of which is perceived loneliness. In this voxel‐based morphometry study, we examined the relationships between perceived loneliness and depression recurrence.MethodsFifty‐two older adults were recruited, and they were split into 3 groups: single episode, multiple episodes, or normal control groups, according to their clinical histories.ResultsThis result suggests the level of functioning regarding the reward system may be negatively related to the number of depressive episodes. Taken together, the findings of this study offer important insight into the neural underpinnings of the course and chronicity of late‐life depression.
Age estimation in Indian adults by the coronal pulp cavity index
Background:Age estimation from tooth coronal index (TCI) using intraoral periapical radiographs by paralleling technique based on a reduction in the size of the dental pulp cavity with advancing age as a result of secondary dentin deposition.Aim and Objectives:The aim of this study is to estimate age for Indian adults using radiographs of mandibular first molar and second premolar teeth using coronal pulp cavity index.Materials and Methods:The study material consists of 400 intraoral periapical radiographs of mandibular second premolar and mandibular first molar from enrolled participants of either gender in the age group of 20–60 years.Statistical Analysis:Data analysis was done using SPSS (Statistical Package for Social Sciences), and Pearson's correlation coefficient (r) was used to find the correlation between age (years) and TCI.Results:TCI was computed for each tooth and regressed on the real age of the sample. The correlation coefficient “r” was −0.865 (for premolar combined sample) and −0.850 (for molar combined sample). The obtained equations were tested on test sample of fifty teeth and age was determined. The absolute mean error between actual and predicted age for premolars was 6.72 months and for molars, it was 9 months.Conclusion:Age estimation using TCI is a precise, noninvasive, less time-consuming, and an inexpensive method.
T cell receptor alpha variable 12‐2 bias in the immunodominant response to Yellow fever virus
AbstractThe repertoire of human αβ T‐cell receptors (TCRs) is generated via somatic recombination of germline gene segments. Despite this enormous variation, certain epitopes can be immunodominant, associated with high frequencies of antigen‐specific T cells and/or exhibit bias toward a TCR gene segment. Here, we studied the TCR repertoire of the HLA‐A*0201‐restricted epitope LLWNGPMAV (hereafter, A2/LLW) from Yellow Fever virus, which generates an immunodominant CD8+ T cell response to the highly effective YF‐17D vaccine. We discover that these A2/LLW‐specific CD8+ T cells are highly biased for the TCR α chain TRAV12‐2. This bias is already present in A2/LLW‐specific naïve T cells before vaccination with YF‐17D. Using CD8+ T cell clones, we show that TRAV12‐2 does not confer a functional advantage on a per cell basis. Molecular modeling indicated that the germline‐encoded complementarity determining region (CDR) 1α loop of TRAV12‐2 critically contributes to A2/LLW binding, in contrast to the conventional dominant dependence on somatically rearranged CDR3 loops. This germline component of antigen recognition may explain the unusually high precursor frequency, prevalence and immunodominance of T‐cell responses specific for the A2/LLW epitope.
The effects of pastoral intensification on the feeding interactions of generalist predators in streams
AbstractLand‐use change can alter trophic interactions with wide‐ranging functional consequences, yet the consequences for aquatic food webs have been little studied. In part, this may reflect the challenges of resolving the diets of aquatic organisms using classical gut contents analysis, especially for soft‐bodied prey. We used next‐generation sequencing to resolve prey use in nearly 400 individuals of two predatory invertebrates (the Caddisfly, Rhyacophila dorsalis, and the Stonefly Dinocras cephalotes) in streams draining land with increasingly intensive livestock farming. Rhyacophila dorsalis occurred in all streams, whereas D. cephalotes was restricted to low intensities, allowing us to test whether: (i) apparent sensitivity to agriculture in the latter species reflects a more specialized diet and (ii) diet in R. dorsalis varied between sites with and without D. cephalotes. DNA was extracted from dissected gut contents, amplified without blocking probes and sequenced using Ion Torrent technology. Both predators were generalists, consuming 30 prey taxa with a preference for taxa that were abundant in all streams or that increased with intensification. Where both predators were present, their diets were nearly identical, and R. dorsalis's diet was virtually unchanged in the absence of D. cephalotes. The loss of D. cephalotes from more intensive sites was probably due to physicochemical stressors, such as sedimentation, rather than to dietary specialization, although wider biotic factors (e.g., competition with other predatory taxa) could not be excluded. This study provides a uniquely detailed description of predator diets along a land‐use intensity gradient, offering new insights into how anthropogenic stressors affect stream communities.
The PiGeOn project: protocol for a longitudinal study examining psychosocial, behavioural and ethical issues and outcomes in cancer tumour genomic profiling
BackgroundGenomic sequencing in cancer (both tumour and germline), and development of therapies targeted to tumour genetic status, hold great promise for improvement of patient outcomes. However, the imminent introduction of genomics into clinical practice calls for better understanding of how patients value, experience, and cope with this novel technology and its often complex results. Here we describe a protocol for a novel mixed-methods, prospective study (PiGeOn) that aims to examine patients’ psychosocial, cognitive, affective and behavioural responses to tumour genomic profiling and to integrate a parallel critical ethical analysis of returning results.MethodsThis is a cohort sub-study of a parent tumour genomic profiling programme enrolling patients with advanced cancer. One thousand patients will be recruited for the parent study in Sydney, Australia from 2016 to 2019. They will be asked to complete surveys at baseline, three, and five months. Primary outcomes are: knowledge, preferences, attitudes and values. A purposively sampled subset of patients will be asked to participate in three semi-structured interviews (at each time point) to provide deeper data interpretation. Relevant ethical themes will be critically analysed to iteratively develop or refine normative ethical concepts or frameworks currently used in the return of genetic information.DiscussionThis will be the first Australian study to collect longitudinal data on cancer patients’ experience of tumour genomic profiling. Findings will be used to inform ongoing ethical debates on issues such as how to effectively obtain informed consent for genomic profiling return results, distinguish between research and clinical practice and manage patient expectations. The combination of quantitative and qualitative methods will provide comprehensive and critical data on how patients cope with ‘actionable’ and ‘non-actionable’ results. This information is needed to ensure that when tumour genomic profiling becomes part of routine clinical care, ethical considerations are embedded, and patients are adequately prepared and supported during and after receiving results.Trial registrationNot required for this sub-study, parent trial registration ACTRN12616000908437.
Murine HPV16 E7-expressing transgenic skin effectively emulates the cellular and molecular features of human high-grade squamous intraepithelial lesions
Currently available vaccines prevent HPV infection and development of HPV-associated malignancies, but do not cure existing HPV infections and dysplastic lesions. Persistence of infection(s) in immunocompetent patients may reflect induction of local immunosuppressive mechanisms by HPV, providing a target for therapeutic intervention. We have proposed that a mouse, expressing HPV16 E7 oncoprotein under a Keratin 14 promoter (K14E7 mice), and which develops epithelial hyperplasia, may assist with understanding local immune suppression mechanisms that support persistence of HPV oncogene-induced epithelial hyperplasia. K14E7 skin grafts recruit immune cells from immunocompetent hosts, but consistently fail to be rejected. Here, we review the literature on HPV-associated local immunoregulation, and compare the findings with published observations on the K14E7 transgenic murine model, including comparison of the transcriptome of human HPV-infected pre-malignancies with that of murine K14E7 transgenic skin. We argue from the similarity of i) the literature findings and ii) the transcriptome profiles that murine K14E7 transgenic skin recapitulates the cellular and secreted protein profiles of high-grade HPV-associated lesions in human subjects. We propose that the K14E7 mouse may be an appropriate model to further study the immunoregulatory effects of HPV E7 expression, and can facilitate development and testing of therapeutic vaccines.
Interaction of childhood urbanicity and variation in dopamine genes alters adult prefrontal function as measured by functional magnetic resonance imaging (fMRI)
Brain phenotypes showing environmental influence may help clarify unexplained associations between urban exposure and psychiatric risk. Heritable prefrontal fMRI activation during working memory (WM) is such a phenotype. We hypothesized that urban upbringing (childhood urbanicity) would alter this phenotype and interact with dopamine genes that regulate prefrontal function during WM. Further, dopamine has been hypothesized to mediate urban-associated factors like social stress. WM-related prefrontal function was tested for main effects of urbanicity, main effects of three dopamine genes—catechol-O-methyltransferase (COMT), dopamine receptor D1 (DRD1), and dopamine receptor D2 (DRD2)—and, importantly, dopamine gene-by-urbanicity interactions. For COMT, three independent human samples were recruited (total n = 487). We also studied 253 subjects genotyped for DRD1 and DRD2. 3T fMRI activation during the N-back WM task was the dependent variable, while childhood urbanicity, dopamine genotype, and urbanicity-dopamine interactions were independent variables. Main effects of dopamine genes and of urbanicity were found. Individuals raised in an urban environment showed altered prefrontal activation relative to those raised in rural or town settings. For each gene, dopamine genotype-by-urbanicity interactions were shown in prefrontal cortex–COMT replicated twice in two independent samples. An urban childhood upbringing altered prefrontal function and interacted with each gene to alter genotype-phenotype relationships. Gene-environment interactions between multiple dopamine genes and urban upbringing suggest that neural effects of developmental environmental exposure could mediate, at least partially, increased risk for psychiatric illness in urban environments via dopamine genes expressed into adulthood.
Emotion Regulation and Complex Brain Networks: Association Between Expressive Suppression and Efficiency in the Fronto-Parietal Network and Default-Mode Network
Emotion regulation (ER) refers to the “implementation of a conscious or non-conscious goal to start, stop or otherwise modulate the trajectory of an emotion” (Etkin et al., 2015). Whereas multiple brain areas have been found to be involved in ER, relatively little is known about whether and how ER is associated with the global functioning of brain networks. Recent advances in brain connectivity research using graph-theory based analysis have shown that the brain can be organized into complex networks composed of functionally or structurally connected brain areas. Global efficiency is one graphic metric indicating the efficiency of information exchange among brain areas and is utilized to measure global functioning of brain networks. The present study examined the relationship between trait measures of ER (expressive suppression (ES) and cognitive reappraisal (CR)) and global efficiency in resting-state functional brain networks (the whole brain network and ten predefined networks) using structural equation modeling (SEM). The results showed that ES was reliably associated with efficiency in the fronto-parietal network and default-mode network. The finding advances the understanding of neural substrates of ER, revealing the relationship between ES and efficient organization of brain networks.
Playground slide-related injuries in preschool children: increased risk of lower extremity injuries when riding on laps
BackgroundThe purpose of this study was to better understand the factors associated with playground slide-related injuries in preschool children and to test the hypothesis that riding on laps increases the likelihood of lower extremity injuries.MethodsPlayground slide-related injuries (product code 1242) in children ≤5 years of age treated in emergency departments from 2002 to 2015 were identified (N = 12,686) using the U.S. Consumer Product Safety Commission’s National Electronic Injury Surveillance System (NEISS). Descriptive and comparative analyses, including chi-square testing and binary logistic regression, were performed.ResultsBased on NEISS stratified national sampling estimates, over 350,000 children ≤5 years of age were injured on slides from 2002 to 2015. Overall, 59% of the children were male, and 65% were white. Almost 60% of injuries occurred in parks or other public areas. The most frequent diagnosis was a fracture (36%); lacerations were 19% of the injuries. A higher proportion of musculoskeletal injuries were seen in toddlers < 3 years old as compared to those 3–5 years of age (p < 0.001). Injuries to the lower extremities increased in frequency as age decreased, whereas injuries to the upper extremities and head/neck/face were more common in older preschoolers. Children < 3 years of age were 12 times more likely to be identified from narratives as being on another person’s lap at the time of injury. Children identified as being on a lap had an increased odds of injury to the lower extremity than to other body parts (OR 43.0, 95% confidence interval (CI) 32.0–58.0), and of lower leg/ankle fracture than fractures elsewhere (OR 49.5, 95% CI 31.7–77.4).ConclusionsDecreasing age was associated with a higher likelihood of being identified as sliding down on another person’s lap and a higher likelihood of lower extremity injuries. Healthcare providers should be mindful of the potential for these slide-related injuries as they can result in a toddler’s fracture of the tibia, which may be occult. Parents should also be made aware of this increased risk and counseled that a child’s foot can catch on the slide’s surfaces when going down on a person’s lap with subsequent twisting forces that can result in a fracture.
Surface display for metabolic engineering of industrially important acetic acid bacteria
Acetic acid bacteria have unique metabolic characteristics that suit them for a variety of biotechnological applications. They possess an arsenal of membrane-bound dehydrogenases in the periplasmic space that are capable of regiospecific and enantioselective partial oxidations of sugars, alcohols, and polyols. The resulting products are deposited directly into the medium where they are easily recovered for use as pharmaceutical precursors, industrial chemicals, food additives, and consumer products. Expression of extracytoplasmic enzymes to augment the oxidative capabilities of acetic acid bacteria is desired but is challenging due to the already crowded inner membrane. To this end, an original surface display system was developed to express recombinant enzymes at the outer membrane of the model acetic acid bacterium Gluconobacter oxydans. Outer membrane porin F (OprF) was used to deliver alkaline phosphatase (PhoA) to the cell surface. Constitutive high-strength p264 and moderate-strength p452 promoters were used to direct expression of the surface display system. This system was demonstrated for biocatalysis in whole-cell assays with the p264 promoter having a twofold increase in PhoA activity compared to the p452 promoter. Proteolytic cleavage of PhoA from the cell surface confirmed proper delivery to the outer membrane. Furthermore, a linker library was constructed to optimize surface display. A rigid (EAAAK)1 linker led to the greatest improvement, increasing PhoA activity by 69%. This surface display system could be used both to extend the capabilities of acetic acid bacteria in current biotechnological processes, and to broaden the potential of these microbes in the production of value-added products.
Developmental abnormalities in supporting cell phalangeal processes and cytoskeleton in the Gjb2 knockdown mouse model
ABSTRACTMutations in the GJB2 gene [which encodes connexin 26 (Cx26)] are the most common causes of hereditary hearing loss in humans, and previous studies showed postnatal development arrest of the organ of Corti in different Cx26-null mouse models. To explore the pathological changes and the mechanism behind the cochlear abnormalities in these mice further, we established transgenic mouse models by conditional knockdown of cochlear Cx26 at postnatal day (P) 0 and P8. Auditory brainstem responses were recorded and the morphological features in the organ of Corti were analyzed 18 days after Cx26 knockdown. Mice in the P0 knockdown group displayed severe hearing loss at all frequencies, whereas mice in the P8 knockdown group showed nearly normal hearing. In the P8 knockdown group, the organ of Corti displayed normal architecture, and no ultrastructural changes were observed. In the P0 knockdown group, the phalangeal processes of Deiter's cells did not develop into finger-like structures, and the formation of microtubules in the pillar cells was significantly reduced; moreover, the amount of acetylated α-tubulin was reduced in pillar cells. Our results indicate that Gjb2 participates in postnatal development of the cytoskeleton in pillar cells during structural maturation of the organ of Corti. In P0 knockdown mice, the reduction in microtubules in pillar cells might be responsible for the failure of the tunnel of Corti to open, and the malformed phalangeal processes might negatively affect the supporting framework of the organ of Corti, which would be a new mechanism of Gjb2-related hearing loss.
Volume-Rendered Projection-Resolved OCT Angiography: 3D Lesion Complexity Is Associated With Therapy Response in Wet Age-Related Macular Degeneration
PurposeTo explore whether quantitative three-dimensional (3D) analysis of choroidal neovascularization (CNV) using projection-resolved optical coherence tomography angiography (PR-OCTA) is associated with treatment response in neovascular age-related macular degeneration (nAMD).MethodsRetrospective, cross-sectional study of 51 eyes of 49 patients undergoing individualized anti-VEGF therapy for nAMD. Patients were classified as “good” or “poor” responders, requiring injections at less or more frequently than 6-week intervals, respectively. Cross-sectional PR-OCTA images were used to measure the distance between Bruch's membrane and highest CNV flow signal. The number of flow layers within the CNV and the distance between these flow layers (CNV flow thickness) were also analyzed. Two masked, independent graders measured the PR-OCTA parameters. We used 3D volume-rendered PR-OCTA to confirm the number of CNV flow layers and further evaluate CNV complexity.ResultsPoor responders had significantly greater distance between Bruch's membrane and highest CNV flow signal (P < 0.01), greater number of CNV flow layers (P = 0.022), and greater CNV flow thickness (P < 0.01). Volume-rendered PR-OCTA images confirmed the number of CNV flow layers.ConclusionsCross-sectional and 3D volume-rendered PR-OCTA provides a novel approach for quantifying CNV complexity. Our results suggest that CNV acquiring more complex 3D vascular structure are associated with more frequent long-term anti-VEGF therapy, reflecting a particular pattern of normalization or complex CNV remodeling process that characterizes these less responsive eyes.
Ehrlichia chaffeensis TRP120 nucleomodulin binds DNA with disordered tandem repeat domain
Ehrlichia chaffeensis, the causative agent of human monocytotropic ehrlichiosis, secretes several effector proteins that bind host DNA to modulate host gene expression. The tandem repeat protein 120 (TRP120), one of the largest effector proteins, has four nearly identical tandem repeat (TR) regions that each consists of 80 amino acids. In addition to playing a role in ehrlichial binding and internalization, TRP120 translocates to the host nucleus where it is thought to function as a transcription factor that modulates gene expression. However, sequence analysis of TRP120 does not identify the presence of DNA-binding or trans-activation domains typical of classical eukaryotic transcription factors. Thus, the mechanism by which TRP120 binds DNA and modulates gene expression remains elusive. Herein, we expressed the TR regions of the TRP120 protein, and characterized its solution structure and ability to bind DNA. TRP120, expressed as either a one or two TR repeat, is a monomer in solution, and is mostly disordered as determined by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. Using NMR spectroscopy, we further show that the 1 TR construct selectively binds GC-rich DNA. Although low pH was required for TRP120 TR-DNA interaction, acidic pH alone does not induce any significant structural changes in the TR region. This suggests that TRP120 folds into an ordered structure upon forming a protein-DNA complex, and thus folding of TRP120 TR is coupled with DNA binding.
Mapping the human brain during a specific Vojta's tactile input: the ipsilateral putamen's role
AbstractA century of research in human brain parcellation has demonstrated that different brain areas are associated with functional tasks. New neuroscientist perspectives to achieve the parcellation of the human brain have been developed to know the brain areas activation and its relationship with different stimuli. This descriptive study aimed to compare brain regions activation by specific tactile input (STI) stimuli according to the Vojta protocol (STI-group) to a non-STI stimulation (non-STI-group). An exploratory functional magnetic resonance imaging (fMRI) study was performed. The 2 groups of participants were passively stimulated by an expert physical therapist using the same paradigm structure, although differing in the place of stimulation. The stimulation was presented to participants using a block design in all cases. A sample of 16 healthy participants, 5 men and 11 women, with mean age 31.31 ± 8.13 years was recruited. Indeed, 12 participants were allocated in the STI-group and 4 participants in the non-STI-group. fMRI was used to map the human brain in vivo while these tactile stimuli were being applied. Data were analyzed using a general linear model in SPM12 implemented in MATLAB. Differences between groups showed a greater activation in the right cortical areas (temporal and frontal lobes), subcortical regions (thalamus, brainstem, and basal nuclei), and in the cerebellum (anterior lobe). STI-group had specific difference brain activation areas, such as the ipsilateral putamen. Future studies should study clinical implications in neurorehabilitation patients.
Metabolic Biomarkers of Ageing in C57BL/6J Wild-Type and Flavin-Containing Monooxygenase 5 (FMO5)-Knockout Mice
It was recently demonstrated in mice that knockout of the flavin-containing monooxygenase 5 gene, Fmo5, slows metabolic ageing via pleiotropic effects. We have now used an NMR-based metabonomics approach to study the effects of ageing directly on the metabolic profiles of urine and plasma from male, wild-type C57BL/6J and Fmo5−/− (FMO5 KO) mice back-crossed onto the C57BL/6J background. The aim of this study was to identify metabolic signatures that are associated with ageing in both these mouse lines and to characterize the age-related differences in the metabolite profiles between the FMO5 KO mice and their wild-type counterparts at equivalent time points. We identified a range of age-related biomarkers in both urine and plasma. Some metabolites, including urinary 6-hydroxy-6-methylheptan-3-one (6H6MH3O), a mouse sex pheromone, showed similar patterns of changes with age, regardless of genetic background. Others, however, were altered only in the FMO5 KO, or only in the wild-type mice, indicating the impact of genetic modifications on mouse ageing. Elevated concentrations of urinary taurine represent a distinctive, ageing-related change observed only in wild-type mice.
Characterising resuscitation promoting factor fluorescent-fusions in mycobacteria
BackgroundResuscitation promoting factor proteins (Rpfs) are peptidoglycan glycosidases capable of resuscitating dormant mycobacteria, and have been found to play a role in the pathogenesis of tuberculosis. However, the specific roles and localisation of each of the 5 Rpfs in Mycobacterium tuberculosis remain mostly unknown. In this work our aim was to construct fluorescent fusions of M. tuberculosis Rpf proteins as tools to investigate their function.ResultsWe found that Rpf-fusions to the fluorescent protein mCherry are functional and able to promote cell growth under different conditions. However, fusions to Enhanced Green Fluorescent Protein (EGFP) were non-functional in the assays used and none were secreted into the extracellular medium, which suggests Rpfs may be secreted via the Sec pathway. No specific cellular localization was observed for either set of fusions using time-lapse video microscopy.ConclusionsWe present the validation and testing of five M. tuberculosis Rpfs fused to mCherry, which are functional in resuscitation assays, but do not show any specific cellular localisation under the conditions tested. Our results suggest that Rpfs are likely to be secreted via the Sec pathway. We propose that such mCherry fusions will be useful tools for the further study of Rpf localisation, individual expression, and function.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1165-0) contains supplementary material, which is available to authorized users.
Correlation of neuropsychological and metabolic changes after epilepsy surgery in patients with left mesial temporal lobe epilepsy with hippocampal sclerosis
BackgroundEpilepsy surgery often causes changes in cognition and cerebral glucose metabolism. Our aim was to explore relationships between pre- and postoperative cerebral metabolism as measured with 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) and neuropsychological test scores in patients with left mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS), who were rendered seizure-free after epilepsy surgery.ResultsThirteen patients were included. All had neuropsychological testing and an interictal FDG-PET scan of the brain pre- and postoperative. Correlations between changes in neuropsychological test scores and metabolism were examined using statistical parametric mapping (SPM). There were no significant changes in the neuropsychological test scores pre- and postoperatively at the group level. Decreased metabolism was observed in the left mesial temporal regions and occipital lobe. Increased metabolism was observed in the bi-frontal and right parietal lobes, temporal lobes, occipital lobes, thalamus, cerebellum, and vermis. In these regions, we did not find a correlation between changes in metabolism and neuropsychological test scores. A significant negative correlation, however, was found between metabolic changes in the precuneus and Boston Naming Test (BNT) scores.ConclusionsThere are significant metabolic decreases in the left mesial temporal regions and increases in the bi-frontal lobes; right parietal, temporal, and occipital lobes; right thalamus; cerebellum; and vermis in patients with left MTLE-HS who were rendered seizure-free after epilepsy surgery. We could not confirm that these changes translate into significant cognitive changes. A significant negative correlation was found between changes in confrontation naming and changes in metabolism in the precuneus. We speculate that the precuneus may play a compensatory role in patients with postoperative naming difficulties after left TLE surgery. Understanding of these neural mechanisms may aid in designing cognitive rehabilitation strategies.Electronic supplementary materialThe online version of this article (10.1186/s13550-018-0385-5) contains supplementary material, which is available to authorized users.
Assessing the efficacy of fathead minnows (Pimephales promelas) for mosquito control
Mosquitoes function as important vectors for many diseases globally and can have substantial negative economic, environmental, and health impacts. Specifically, West Nile virus (WNv) is a significant and increasing threat to wildlife populations and human health throughout North America. Mosquito control is an important means of controlling the spread of WNv, as the virus is primarily spread between avian and mosquito vectors. This is of particular concern for avian host species such as the Greater sage-grouse (Centrocercus urophasianus), in which WNv negatively impacts fitness parameters. Most mosquito control methods focus on the larval stages. In North America, control efforts are largely limited to larvicides, which require repeated application and have potentially negative ecological impacts. There are multiple potential advantages to using indigenous fish species as an alternative for larval control including lowered environmental impact, decreased costs in terms of time and financial inputs, and the potential for the establishment of self-sustaining fish populations. We tested the efficacy of using fathead minnows (Pimephales promelas) as biological control for mosquito populations in livestock reservoirs of semiarid rangelands. We introduced minnows into 10 treatment reservoirs and monitored an additional 6 non-treated reservoirs as controls over 3 years. Adult mosquitoes of species known to transmit WNv (e.g., Culex tarsalis) were captured at each site and mosquito larvae were also present at all sites. Stable isotope analysis confirmed that introduced fathead minnows were feeding at the mosquito larvae trophic level in all but one treatment pond. Treatment ponds demonstrated suppressed levels of mosquito larva over each season compared to controls with a model-predicted 114% decrease in larva density within treatment ponds. Minnows established self-sustaining populations throughout the study in all reservoirs that maintained sufficient water levels. Minnow survival was not influenced by water quality. Though minnows did not completely eradicate mosquito larvae, minnows are a promising alternative to controlling mosquito larvae density within reservoirs. We caution that careful site selection is critical to avoid potential negative impacts, but suggest the introduction of fathead minnows in reservoirs can dramatically reduce mosquito larva abundance and potentially help mitigate vector-borne disease transmission.
TRPV4 inhibition attenuates stretch-induced inflammatory cellular responses and lung barrier dysfunction during mechanical ventilation
Mechanical ventilation is an important tool for supporting critically ill patients but may also exert pathological forces on lung cells leading to Ventilator-Induced Lung Injury (VILI). We hypothesised that inhibition of the force-sensitive transient receptor potential vanilloid (TRPV4) ion channel may attenuate the negative effects of mechanical ventilation. Mechanical stretch increased intracellular Ca2+ influx and induced release of pro-inflammatory cytokines in lung epithelial cells that was partially blocked by about 30% with the selective TRPV4 inhibitor GSK2193874, but nearly completely blocked with the pan-calcium channel blocker ruthenium red, suggesting the involvement of more than one calcium channel in the response to mechanical stress. Mechanical stretch also induced the release of pro-inflammatory cytokines from M1 macrophages, but in contrast this was entirely dependent upon TRPV4. In a murine ventilation model, TRPV4 inhibition attenuated both pulmonary barrier permeability increase and pro-inflammatory cytokines release due to high tidal volume ventilation. Taken together, these data suggest TRPV4 inhibitors may have utility as a prophylactic pharmacological treatment to improve the negative pathological stretch-response of lung cells during ventilation and potentially support patients receiving mechanical ventilation.
The Effect of a Nonpeptide Angiotensin II Type 2 Receptor Agonist, Compound 21, on Aortic Aneurysm Growth in a Mouse Model of Marfan Syndrome
Introduction:Available evidence suggests that the renin–angiotensin–aldosterone (RAA) system is a good target for medical intervention on aortic root dilatation in Marfan syndrome (MFS). The effect of Compound 21 (C21), a nonpeptide angiotensin II type 2 receptor agonist, on aneurysm progression was tested.Methods:Mice with a mutation in fibrillin-1 (Fbn1C1039G/+) and wild-type mice were treated with vehicle, losartan, C21, enalapril, or a combination. Blood pressure, aortic root diameter, and histological slides were evaluated.Results:All groups had a comparable blood pressure. Echographic evaluation of the aortic root diameter revealed a protective effect of angiotensin II type 1 receptor antagonist (losartan) and no effect of C21 treatment. None of the treatments had a beneficial effect on the histological changes in MFS.Discussion:This study confirms that angiotensin II type 1 receptor antagonism (losartan) decreases aortic aneurysm growth in a mouse model of MFS. A nonpeptide angiotensin II type 2 receptor agonist (C21), at the doses studied, was ineffective. Future studies are warranted to further elucidate the exact role of the RAA system in aneurysm formation in MFS and identify alternative targets for intervention.
A Vegetal Biopolymer-Based Biostimulant Promoted Root Growth in Melon While Triggering Brassinosteroids and Stress-Related Compounds
Plant biostimulants are receiving great interest for boosting root growth during the first phenological stages of vegetable crops. The present study aimed at elucidating the morphological, physiological, and metabolomic changes occurring in greenhouse melon treated with the biopolymer-based biostimulant Quik-link, containing lateral root promoting peptides, and lignosulphonates. The vegetal-based biopolymer was applied at five rates (0, 0.06, 0.12, 0.24, or 0.48 mL plant-1) as substrate drench. The application of biopolymer-based biostimulant at 0.12 and 0.24 mL plant-1 enhanced dry weight of melon leaves and total biomass by 30.5 and 27.7%, respectively, compared to biopolymer applications at 0.06 mL plant-1 and untreated plants. The root dry biomass, total root length, and surface in biostimulant-treated plants were significantly higher at 0.24 mL plant-1 and to a lesser extent at 0.12 and 0.48 mL plant-1, in comparison to 0.06 mL plant-1 and untreated melon plants. A convoluted biochemical response to the biostimulant treatment was highlighted through UHPLC/QTOF-MS metabolomics, in which brassinosteroids and their interaction with other hormones appeared to play a pivotal role. Root metabolic profile was more markedly altered than leaves, following application of the biopolymer-based biostimulant. Brassinosteroids triggered in roots could have been involved in changes of root development observed after biostimulant application. These hormones, once transported to shoots, could have caused an hormonal imbalance. Indeed, the involvement of abscisic acid, cytokinins, and gibberellin related compounds was observed in leaves following root application of the biopolymer-based biostimulant. Nonetheless, the treatment triggered an accumulation of several metabolites involved in defense mechanisms against biotic and abiotic stresses, such as flavonoids, carotenoids, and glucosinolates, thus potentially improving resistance toward plant stresses.
Reduced reward‐related neural response to mimicry in individuals with autism
AbstractMimicry is a facilitator of social bonds in humans, from infancy. This facilitation is made possible through changing the reward value of social stimuli; for example, we like and affiliate more with people who mimic us. Autism spectrum disorders (ASD) are marked by difficulties in forming social bonds. In this study, we investigate whether the reward‐related neural response to being mimicked is altered in individuals with ASD, using a simple conditioning paradigm. Multiple studies in humans and nonhuman primates have established a crucial role for the ventral striatal (VS) region in responding to rewards. In this study, adults with ASD and matched controls first underwent a conditioning task outside the scanner, where they were mimicked by one face and ‘anti‐mimicked’ by another. In the second part, participants passively viewed the conditioned faces in a 3T MRI scanner using a multi‐echo sequence. The differential neural response towards mimicking vs. anti‐mimicking faces in the VS was tested for group differences as well as an association with self‐reported autistic traits. Multiple regression analysis revealed lower left VS response to mimicry (mimicking > anti‐mimicking faces) in the ASD group compared to controls. The VS response to mimicry was negatively correlated with autistic traits across the whole sample. Our results suggest that for individuals with ASD and high autistic traits, being mimicked is associated with lower reward‐related neural response. This result points to a potential mechanism underlying the difficulties reported by many of individuals with ASD in building social rapport.
Genome-Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds
Reproduction is an important trait in sheep breeding as well as in other livestock. However, despite its importance the genetic mechanisms of litter size in domestic sheep (Ovis aries) are still poorly understood. To explore genetic mechanisms underlying the variation in litter size, we conducted multiple independent genome-wide association studies in five sheep breeds of high prolificacy (Wadi, Hu, Icelandic, Finnsheep, and Romanov) and one low prolificacy (Texel) using the Ovine Infinium HD BeadChip, respectively. We identified different sets of candidate genes associated with litter size in different breeds: BMPR1B, FBN1, and MMP2 in Wadi; GRIA2, SMAD1, and CTNNB1 in Hu; NCOA1 in Icelandic; INHBB, NF1, FLT1, PTGS2, and PLCB3 in Finnsheep; ESR2 in Romanov and ESR1, GHR, ETS1, MMP15, FLI1, and SPP1 in Texel. Further annotation of genes and bioinformatics analyses revealed that different biological pathways could be involved in the variation in litter size of females: hormone secretion (FSH and LH) in Wadi and Hu, placenta and embryonic lethality in Icelandic, folliculogenesis and LH signaling in Finnsheep, ovulation and preovulatory follicle maturation in Romanov, and estrogen and follicular growth in Texel. Taken together, our results provide new insights into the genetic mechanisms underlying the prolificacy trait in sheep and other mammals, suggesting targets for selection where the aim is to increase prolificacy in breeding projects.
Caregiver burden and caregiver appraisal of psychiatric symptoms are not modulated by subthalamic deep brain stimulation for Parkinson’s disease
Subthalamic deep brain stimulation is an advanced therapy that typically improves quality of life for persons with Parkinson’s disease (PD). However, the effect on caregiver burden is unclear. We recruited 64 persons with PD and their caregivers from a movement disorders clinic during the assessment of eligibility for subthalamic DBS. We used clinician-, patient- and caregiver-rated instruments to follow the patient–caregiver dyad from pre- to postoperative status, sampling repeatedly in the postoperative period to ascertain fluctuations in phenotypic variables. We employed multivariate models to identify key drivers of burden. We clustered caregiver-rated variables into ‘high’ and ‘low’ symptom groups and examined whether postoperative cluster assignment could be predicted from baseline values. Psychiatric symptoms in the postoperative period made a substantial contribution to longitudinal caregiver burden. The development of stimulation-dependent mood changes was also associated with increased burden. However, caregiver burden and caregiver-rated psychiatric symptom clusters were temporally stable and thus predicted only by their baseline values. We confirmed this finding using frequentist and Bayesian statistics, concluding that in our sample, subthalamic DBS for PD did not significantly influence caregiver burden or caregiver-rated psychiatric symptoms. Specifically, patient–caregiver dyads with high burden and high levels of psychiatric symptoms at baseline were likely to maintain this profile during follow-up. These findings support the importance of assessing caregiver burden prior to functional neurosurgery. Furthermore, they suggest that interventions addressing caregiver burden in this population should target those with greater symptomatology at baseline and may usefully prioritise psychiatric symptoms reported by the caregiver.
Association of Decreased Percentage of Vδ2+Vγ9+ γδ T Cells With Disease Severity in Multiple Sclerosis
We recently reported that deletion-type copy number variations of the T cell receptor (TCR) γ, α, and δ genes greatly enhanced susceptibility to multiple sclerosis (MS). However, the effect of abnormal TCR γδ gene rearrangement on MS pathogenesis remains unknown. In the present study, we aimed to clarify γδ TCR repertoire alterations and their relationship to clinical and immunological parameters in MS patients by comprehensive flow cytometric immunophenotyping. Peripheral blood mononuclear cells obtained from 30 untreated MS patients in remission and 23 age- and sex-matched healthy controls (HCs) were stained for surface markers and intracellular cytokines after stimulation with phorbol 12-myristate 13-acetate and ionomycin, and analyzed by flow cytometry. MS patients showed significantly decreased percentages of Vδ2+ and Vδ2+Vγ9+ cells in γδ T cells (pcorr = 0.0297 and pcorr = 0.0288, respectively) and elevated Vδ1/Vδ2 ratios compared with HCs (p = 0.0033). The percentages of interferon (IFN)-γ+Vδ2+ and interleukin (IL)-17A+IFN-γ+Vδ2+ cells in γδ T cells, as well as IFN-γ+ cells in Vδ2+ γδ T cells, were significantly lower in MS patients than in HCs (pcorr < 0.0009, pcorr = 0.0135, and pcorr = 0.0054, respectively). The percentages of Vδ2+ and Vδ2+Vγ9+ cells in γδ T cells were negatively correlated with both the Expanded Disability Status Scale score (r = −0.5006, p = 0.0048; and r = −0.5040, p = 0.0045, respectively) and Multiple Sclerosis Severity Score (r = –0.4682, p = 0.0091; and r = –0.4706, p = 0.0087, respectively), but not with age at disease onset, disease duration, or annualized relapse rate. In HCs, the percentages of Vδ2+ and Vδ2+Vγ9+ cells of total CD3+ T cells had strong positive correlations with the percentage of CD25+CD127low/− cells in CD4+ T cells (r = 0.7826, p < 0.0001; and r = 0.7848, p < 0.0001, respectively), whereas such correlations were totally absent in MS patients. These findings suggest that decreased Vδ2+Vγ9+ γδ T cells are associated with disability in MS. Therefore, the Vδ1/Vδ2 ratio might be a candidate biomarker for predicting disease severity in MS.
Functional connectivity in dementia with Lewy bodies: A within‐ and between‐network analysis
AbstractDementia with Lewy bodies (DLB) is a common form of dementia and is characterized by cognitive fluctuations, visual hallucinations, and Parkinsonism. The phenotypic expression of the disease may, in part, relate to alterations in functional connectivity within and between brain networks. This resting‐state study sought to clarify this in DLB, how networks differed from Alzheimer's disease (AD), and whether they were related to clinical symptoms in DLB. Resting‐state networks were estimated using independent component analysis. We investigated functional connectivity changes in 31 DLB patients compared to 31 healthy controls and a disease comparator group of 29 AD patients using dual regression and FSLNets. Within‐network connectivity was generally decreased in DLB compared to controls, mainly in motor, temporal, and frontal networks. Between‐network connectivity was mainly intact; only the connection between a frontal and a temporal network showed increased connectivity in DLB. Differences between AD and DLB were subtle and we did not find any significant correlations with the severity of clinical symptoms in DLB. This study emphasizes the importance of reduced connectivity within motor, frontal, and temporal networks in DLB with relative sparing of the default mode network. The lack of significant correlations between connectivity measures and clinical scores indicates that the observed reduced connectivity within these networks might be related to the presence, but not to the severity of motor and cognitive impairment in DLB patients. Furthermore, our results suggest that AD and DLB may show more similarities than differences in patients with mild disease.
Model‐driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation
SummaryThe abundance of the human intestinal symbiont Akkermansia muciniphila has found to be inversely correlated with several diseases, including metabolic syndrome and obesity. A. muciniphila is known to use mucin as sole carbon and nitrogen source. To study the physiology and the potential for therapeutic applications of this bacterium, we designed a defined minimal medium. The composition of the medium was based on the genome‐scale metabolic model of A. muciniphila and the composition of mucin. Our results indicate that A. muciniphila does not code for GlmS, the enzyme that mediates the conversion of fructose‐6‐phosphate (Fru6P) to glucosamine‐6‐phosphate (GlcN6P), which is essential in peptidoglycan formation. The only annotated enzyme that could mediate this conversion is Amuc‐NagB on locus Amuc_1822. We found that Amuc‐NagB was unable to form GlcN6P from Fru6P at physiological conditions, while it efficiently catalyzed the reverse reaction. To overcome this inability, N‐acetylglucosamine needs to be present in the medium for A. muciniphila growth. With these findings, the genome‐scale metabolic model was updated and used to accurately predict growth of A. muciniphila on synthetic media. The finding that A. muciniphila has a necessity for GlcNAc, which is present in mucin further prompts the adaptation to its mucosal niche.
Optic radiation injury in patients with aneurismal subarachnoid hemorrhage: A preliminary diffusion tensor imaging report
Visual field defect is one of the various clinical manifestations in patients with subarachnoid hemorrhage (SAH). Little is known about the pathogenic mechanism of visual field defect in SAH. In the current study, we investigated the diffusion tensor imaging (DTI) finding of the optic radiation in patients with SAH following rupture of a cerebral artery aneurysm. We recruited 21 patients with aneurismal SAH (12 males, 9 females, mean age, 52.67 years; range, 41–68 years) who showed no definite lesion along the visual pathway. Twenty-one age-and sex-matched normal control subjects were also recruited. DTI data were acquired at an average of 5.9 weeks (range: 3–12 weeks) after onset and reconstruction of the optic radiation was performed using DTI-Studio software. The fractional anisotropy value, apparent diffusion coefficient value, and fiber number of the optic radiation were measured. The fractional anisotropy value of the optic radiation was significantly decreased, and the apparent diffusion coefficient value was significantly increased, in patients with aneurismal SAH than in normal control subjects. However, there was no significant difference in the fiber number of the optic radiation between patients with aneurismal SAH and normal control subjects. The decrement of fractional anisotropy value and increment of apparent diffusion coefficient value of the optic radiation in patients with aneurismal SAH suggest optic radiation injury. Therefore, we recommend a thorough evaluation for optic radiation injury in patient with aneurismal SAH.
A direct regulatory link between microRNA-137 and SHANK2: implications for neuropsychiatric disorders
BackgroundMutations in the SHANK genes, which encode postsynaptic scaffolding proteins, have been linked to a spectrum of neurodevelopmental disorders. The SHANK genes and the schizophrenia-associated microRNA-137 show convergence on several levels, as they are both expressed at the synapse, influence neuronal development, and have a strong link to neurodevelopmental and neuropsychiatric disorders like intellectual disability, autism, and schizophrenia. This compiled evidence raised the question if the SHANKs might be targets of miR-137.MethodsIn silico analysis revealed a putative binding site for microRNA-137 (miR-137) in the SHANK2 3′UTR, while this was not the case for SHANK1 and SHANK3. Luciferase reporter assays were performed by overexpressing wild type and mutated SHANK2-3′UTR and miR-137 in human neuroblastoma cells and mouse primary hippocampal neurons. miR-137 was also overexpressed or inhibited in hippocampal neurons, and Shank2 expression was analyzed by quantitative real-time PCR and Western blot. Additionally, expression levels of experimentally validated miR-137 target genes were analyzed in the dorsolateral prefrontal cortex (DLPFC) of schizophrenia and control individuals using the RNA-Seq data from the CommonMind Consortium.ResultsmiR-137 directly targets the 3′UTR of SHANK2 in a site-specific manner. Overexpression of miR-137 in mouse primary hippocampal neurons significantly lowered endogenous Shank2 protein levels without detectable influence on mRNA levels. Conversely, miR-137 inhibition increased Shank2 protein expression, indicating that miR-137 regulates SHANK2 expression by repressing protein translation rather than inducing mRNA degradation.To find out if the miR-137 signaling network is altered in schizophrenia, we compared miR-137 precursor and miR-137 target gene expression in the DLPFC of schizophrenia and control individuals using the CommonMind Consortium RNA sequencing data. Differential expression of 23% (16/69) of known miR-137 target genes was detected in the DLPFC of schizophrenia individuals compared with controls. We propose that in further targets (e.g., SHANK2, as described in this paper) which are not regulated on RNA level, effects may only be detectable on protein level.ConclusionOur study provides evidence that a direct regulatory link exists between miR-137 and SHANK2 and supports the finding that miR-137 signaling might be altered in schizophrenia.Electronic supplementary materialThe online version of this article (10.1186/s11689-018-9233-1) contains supplementary material, which is available to authorized users.
Differential Medial Temporal Lobe and Parietal Cortical Contributions to Real-world Autobiographical Episodic and Autobiographical Semantic Memory
Autobiographical remembering can depend on two forms of memory: episodic (event) memory and autobiographical semantic memory (remembering personally relevant semantic knowledge, independent of recalling a specific experience). There is debate about the degree to which the neural signals that support episodic recollection relate to or build upon autobiographical semantic remembering. Pooling data from two fMRI studies of memory for real-world personal events, we investigated whether medial temporal lobe (MTL) and parietal subregions contribute to autobiographical episodic and semantic remembering. During scanning, participants made memory judgments about photograph sequences depicting past events from their life or from others’ lives, and indicated whether memory was based on episodic or semantic knowledge. Results revealed several distinct functional patterns: activity in most MTL subregions was selectively associated with autobiographical episodic memory; the hippocampal tail, superior parietal lobule, and intraparietal sulcus were similarly engaged when memory was based on retrieval of an autobiographical episode or autobiographical semantic knowledge; and angular gyrus demonstrated a graded pattern, with activity declining from autobiographical recollection to autobiographical semantic remembering to correct rejections of novel events. Collectively, our data offer insights into MTL and parietal cortex functional organization, and elucidate circuitry that supports different forms of real-world autobiographical memory.
Deep intraspecific DNA barcode splits and hybridisation in the Udeaalpinalis group (Insecta, Lepidoptera, Crambidae) – an integrative revision
AbstractThe analysis of mitochondrial COI data for the European-Centroasian montane Udeaalpinalis species group finds deep intraspecific splits. Specimens of U.austriacalis and U.rhododendronalis separate into several biogeographical groups. These allopatric groups are not recovered in the analyses of the two nuclear markers wingless and Elongation factor 1-alpha, except for U.austriacalis from the Pyrenees and the French Massif Central. The latter populations are also morphologically distinct and conspecific with Scopuladonzelalis Guenée, 1854, which is removed from synonymy and reinstated as Udeadonzelalis (Guenée, 1854) stat. rev. Furthermore, Udeaaltaica (Zerny, 1914), stat. n. from the Mongolian central Altai mountains, U.juldusalis (Zerny, 1914), stat. n. from the Tian Shan mountains of Kazakhstan, Kyrgyzstan and NW China, and U.plumbalis (Zerny, 1914), stat. n. from the Sayan Mountains of Northern Mongolia are raised to species level, and lectotypes are designated. Evidence of introgression of U.alpinalis into U.uliginosalis at three localities in the Central Alps is presented. A screening for Wolbachia using the markers wsp, gatB and ftsZ was negative for the U.alpinalis species group, but Wolbachia was found in single specimens of U.fulvalis and U.olivalis (both in the U.numeralis species group). We do not find evidence for the conjecture of several authors of additional subspecies in U.rhododendronalis, and synonymise U.rhododendronalisluquetalis Leraut, 1996, syn. n. and U.r.ventosalis Leraut, 1996, syn. n. with the nominal U.rhododendronalis (Duponchel, 1834).
Mapping a male-fertility restoration locus for the A4 cytoplasmic-genic male-sterility system in pearl millet using a genotyping-by-sequencing-based linkage map
BackgroundPearl millet (Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) R. Br) is an important cereal and fodder crop in hot and arid environments. There is great potential to improve pearl millet production through hybrid breeding. Cytoplasmic male sterility (CMS) and the corresponding nuclear fertility restoration / sterility maintenance genes (Rfs) are essential tools for economic hybrid seed production in pearl millet. Mapping the Rf genes of the A4 CMS system in pearl millet would enable more efficient introgression of both dominant male-fertility restoration alleles (Rf) and their recessive male-sterility maintenance counterparts (rf).ResultsA high density linkage map based on single nucleotide polymorphism (SNP) markers was generated using an F2 mapping population and genotyping-by-sequencing (GBS). The parents of this cross were ‘ICMA 02777’ and ‘ICMR 08888’, which segregate for the A4Rf locus. The linkage map consists of 460 SNP markers distributed mostly evenly and has a total length of 462 cM. The segregation ratio of male-fertile and male-sterile plants (3:1) based on pollen production (presence/absence) indicated monogenic dominant inheritance of male-fertility restoration. Correspondingly, a major quantitative trait locus (QTL) for pollen production was found on linkage group 2, with cross-validation showing a very high QTL occurrence (97%). The major QTL was confirmed using selfed seed set as phenotypic trait, though with a lower precision. However, these QTL explained only 14.5% and 9.9% of the phenotypic variance of pollen production and selfed seed set, respectively, which was below expectation. Two functional KASP markers were developed for the identified locus.ConclusionThis study identified a major QTL for male-fertility restoration using a GBS-based linkage map and developed KASP markers which support high-throughput screening of the haploblock. This is a first step toward marker-assisted selection of A4 male-fertility restoration and male-sterility maintenance in pearl millet.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1267-8) contains supplementary material, which is available to authorized users.
Classical NF-κB Metabolically Reprograms Sarcoma Cells Through Regulation of Hexokinase 2
BackgroundMetabolic reprogramming has emerged as a cancer hallmark, and one of the well-known cancer-associated metabolic alterations is the increase in the rate of glycolysis. Recent reports have shown that both the classical and alternative signaling pathways of nuclear factor κB (NF-κB) play important roles in controlling the metabolic profiles of normal cells and cancer cells. However, how these signaling pathways affect the metabolism of sarcomas, specifically rhabdomyosarcoma (RMS) and osteosarcoma (OS), has not been characterized.MethodsClassical NF-κB activity was inhibited through overexpression of the IκBα super repressor of NF-κB in RMS and OS cells. Global gene expression analysis was performed using Affymetrix GeneChip Human Transcriptome Array 2.0, and data were interpreted using gene set enrichment analysis. Seahorse Bioscience XFe24 was used to analyze oxygen consumption rate as a measure of aerobic respiration.ResultsInhibition of classical NF-κB activity in sarcoma cell lines restored alternative signaling as well as an increased oxidative respiratory metabolic phenotype in vitro. In addition, microarray analysis indicated that inhibition of NF-κB in sarcoma cells reduced glycolysis. We showed that a glycolytic gene, hexokinase (HK) 2, is a direct NF-κB transcriptional target. Knockdown of HK2 shifted the metabolic profile in sarcoma cells away from aerobic glycolysis, and re-expression of HK2 rescued the metabolic shift induced by inhibition of NF-κB activity in OS cells.ConclusionThese findings suggest that classical signaling of NF-κB plays a crucial role in the metabolic profile of pediatric sarcomas potentially through the regulation of HK2.
Personalized Hydration Strategy Attenuates the Rise in Heart Rate and in Skin Temperature Without Altering Cycling Capacity in the Heat
The optimal hydration plan [i.e., drink to thirst, ad libitum (ADL), or personalized plan] to be adopted during exercise in recreational athletes has recently been a matter of debate and, due to conflicting results, consensus does not exist. In the present investigation, we tested whether a personalized hydration strategy based on sweat rate would affect cardiovascular and thermoregulatory responses and exercise capacity in the heat. Eleven recreational male cyclists underwent two familiarization cycling sessions in the heat (34°C, 40% RH) where sweat rate was also determined. A fan was used to enhance sweat evaporation. Participants then performed three randomized time-to-exhaustion (TTE) trials in the heat with different hydration strategies: personalized volume (PVO), where water was consumed, based on individual sweat rate, every 10 min; ADL, where free access to water was allowed; and a control (CON) trial with no fluids. Blood osmolality and urine-specific gravity were measured before each trial. Heart rate (HR), rectal, and skin temperatures were monitored throughout trials. Time to exhaustion at 70% of maximal workload was used to define exercise capacity in the heat, which was similar in all trials (p = 0.801). Body mass decreased after ADL (p = 0.008) and CON (p < 0.001) and was maintained in PVO trials (p = 0.171). Participants consumed 0 ml in CON, 166 ± 167 ml in ADL, and 1,080 ± 166 ml in PVO trials. The increase in mean body temperature was similar among trials despite a lower increase in skin temperature during PVO trial in comparison with CON (2.1 ± 0.6 vs. 2.9 ± 0.5°C, p = 0.0038). HR was lower toward the end of TTE in PVO (162 ± 8 bpm) in comparison with ADL (168 ± 12 bpm) and CON (167 ± 10 bpm), p < 0.001. In conclusion, a personalized hydration strategy can reduce HR during a moderate to high intensity exercise session in the heat and halt the increase in skin temperature. Despite these advantages, cycling capacity in the heat remained unchanged.
Cognitive Function and Brain Atrophy Predict Non-pharmacological Efficacy in Dementia: The Mihama-Kiho Scan Project2
We aimed to determine whether neuropsychological deficits and brain atrophy could predict the efficacy of non-pharmacological interventions. Forty-six participants with mild-to-moderate dementia were monitored for 6 months; 25 underwent an intervention involving physical exercise with music, and 21 performed cognitive stimulation tasks. Participants were categorized into improvement (IMP) and no-IMP subgroups. In the exercise-with-music group, the no-IMP subgroup performed worse than the IMP subgroup on the Rivermead Behavioural Memory Test at baseline. In the cognitive-stimulation group, the no-IMP subgroup performed worse than the IMP subgroup on Raven’s Colored Progressive Matrices and the cognitive functional independence measure at baseline. In the no-IMP subgroup, voxel-based morphometric analysis at baseline revealed more extensive gray matter loss in the anterior cingulate gyrus and left middle frontal gyrus in the exercise-with-music and cognitive-stimulation groups, respectively. Participants with mild-to-moderate dementia with cognitive decline and extensive cortical atrophy are less likely to show improved cognitive function after non-pharmaceutical therapy.
A distinct species, Dodonaformosana, detected in the Dodonaeugenes species complex: clarification of the taxonomic status of the Punch butterfly in Taiwan
AbstractThe Tailed Punch, Dodonaeugenes, is widely distributed in East Asia with seven subspecies currently recognized. However, two of them, namely ssp. formosana and ssp. esakii found in Taiwan, are hard to distinguish from each other due to ambiguous diagnostic characters. In this study, their taxonomic status is clarified by comparing genitalia characters and phylogenetic relationships based on mitochondrial sequences, COI and COII (total 2211 bps). Our results show that there is no reliable feature to separate these two subspecies. Surprisingly we found that Dodona in Taiwan is more closely related to the Orange Punch, D.egeon, than to other subspecies of D.eugenes. Therefore, the following nomenclatural changes are proposed: Dodonaeugenesformosana is revised to specific status as Dodonaformosana Matsumura, 1919, stat. rev, and ssp. esakii is sunk to a junior synonym of Dodonaformosanasyn. n.
A new species of the genus Pseudocrangonyx (Crustacea, Amphipoda, Pseudocrangonyctidae) from Korea
AbstractA new subterranean species of pseudocrangonyctid amphipod, Pseudocrangonyxdaejeonensissp. n. is described from the interstitial waters in Daejeon, Korea. Pseudocrangonyxdaejeonensissp. n. is distinguished from three morphologically similar congeners, P.coreanus Uéno, 1966, P.febras Sidorov, 2009, and P.gudariensis Tomikawa & Sato, 2016, by the characteristics of antenna 1, antenna 2, mandible, gnathopod 2, pleopods, uropods 1–2, and telson. Molecular phylogenetic analyses based on nuclear 28S rRNA and histone H3, and mitochondrial cytochrome c oxidase subunit I and 16S rRNA genes revealed that P.daejeonensis is a sister species of the unnamed Pseudocrangonyx sp. 3 inhabiting central Japan.
The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes
AbstractThe world’s smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development.
Metabolic characterization of isocitrate dehydrogenase (IDH) mutant and IDH wildtype gliomaspheres uncovers cell type-specific vulnerabilities
BackgroundThere is considerable interest in defining the metabolic abnormalities of IDH mutant tumors to exploit for therapy. While most studies have attempted to discern function by using cell lines transduced with exogenous IDH mutant enzyme, in this study, we perform unbiased metabolomics to discover metabolic differences between a cohort of patient-derived IDH1 mutant and IDH wildtype gliomaspheres.MethodsUsing both our own microarray and the TCGA datasets, we performed KEGG analysis to define pathways differentially enriched in IDH1 mutant and IDH wildtype cells and tumors. Liquid chromatography coupled to mass spectrometry analysis with labeled glucose and deoxycytidine tracers was used to determine differences in overall cellular metabolism and nucleotide synthesis. Radiation-induced DNA damage and repair capacity was assessed using a comet assay. Differences between endogenous IDH1 mutant metabolism and that of IDH wildtype cells transduced with the IDH1 (R132H) mutation were also investigated.ResultsOur KEGG analysis revealed that IDH wildtype cells were enriched for pathways involved in de novo nucleotide synthesis, while IDH1 mutant cells were enriched for pathways involved in DNA repair. LC-MS analysis with fully labeled 13C-glucose revealed distinct labeling patterns between IDH1 mutant and wildtype cells. Additional LC-MS tracing experiments confirmed increased de novo nucleotide synthesis in IDH wildtype cells relative to IDH1 mutant cells. Endogenous IDH1 mutant cultures incurred less DNA damage than IDH wildtype cultures and sustained better overall growth following X-ray radiation. Overexpression of mutant IDH1 in a wildtype line did not reproduce the range of metabolic differences observed in lines expressing endogenous mutations, but resulted in depletion of glutamine and TCA cycle intermediates, an increase in DNA damage following radiation, and a rise in intracellular ROS.ConclusionsThese results demonstrate that IDH1 mutant and IDH wildtype cells are easily distinguishable metabolically by analyzing expression profiles and glucose consumption. Our results also highlight important differences in nucleotide synthesis utilization and DNA repair capacity that could be exploited for therapy. Altogether, this study demonstrates that IDH1 mutant gliomas are a distinct subclass of glioma with a less malignant, but also therapy-resistant, metabolic profile that will likely require distinct modes of therapy.Electronic supplementary materialThe online version of this article (10.1186/s40170-018-0177-4) contains supplementary material, which is available to authorized users.
Cranioplasty After Severe Traumatic Brain Injury: Effects of Trauma and Patient Recovery on Cranioplasty Outcome
BackgroundIn patients with severe traumatic brain injury (sTBI) treated with decompressive craniectomy (DC), factors affecting the success of later cranioplasty are poorly known.ObjectiveWe sought to investigate if injury- and treatment-related factors, and state of recovery could predict the risk of major complications in cranioplasty requiring implant removal, and how these complications affect the outcome.MethodsA retrospective cohort of 40 patients with DC following sTBI and subsequent cranioplasty was studied. Non-injury-related factors were compared with a reference population of 115 patients with DC due to other conditions.ResultsOutcome assessed 1 day before cranioplasty did not predict major complications leading to implant removal. Successful cranioplasty was associated with better outcome, whereas a major complication attenuates patient recovery: in patients with favorable outcome assessed 1 year after cranioplasty, major complication rate was 7%, while in patients with unfavorable outcome the rate was 42% (p = 0.003). Of patients with traumatic subarachnoid hemorrhage (tSAH) on admission imaging 30% developed a major complication, while none of patients without tSAH had a major complication (p = 0.014). Other imaging findings, age, admission Glasgow Coma Scale, extracranial injuries, length of stay at intensive care unit, cranioplasty materials, and timing of cranioplasty were not associated with major complications.ConclusionA successful cranioplasty after sTBI and DC predicts favorable outcome 1 year after cranioplasty, while stage of recovery before cranioplasty does not predict cranioplasty success or failure. tSAH on admission imaging is a major risk factor for a major complication leading to implant removal.
Cognitive Behavioral Therapy Is Associated With Enhanced Cognitive Control Network Activity in Major Depression and Posttraumatic Stress Disorder
BACKGROUNDBoth major depressive disorder (MDD) and posttraumatic stress disorder (PTSD) are characterized by depressive symptoms, abnormalities in brain regions important for cognitive control, and response to cognitive behavioral therapy (CBT). However, whether a common neural mechanism underlies CBT response across diagnoses is unknown.METHODSBrain activity during a cognitive control task was measured using functional magnetic resonance imaging in 104 participants: 28 patients with MDD, 53 patients with PTSD, and 23 healthy control subjects; depression and anxiety symptoms were determined on the same day. A patient subset (n = 31) entered manualized CBT and, along with controls (n = 19), was rescanned at 12 weeks. Linear mixed effects models assessed the relationship between depression and anxiety symptoms and brain activity before and after CBT.RESULTSAt baseline, activation of the left dorsolateral prefrontal cortex was negatively correlated with Montgomery–Åsberg Depression Rating Scale scores across all participants; this brain–symptom association did not differ between MDD and PTSD. Following CBT treatment of patients, regions within the cognitive control network, including ventrolateral prefrontal cortex and dorsolateral prefrontal cortex, showed a significant increase in activity.CONCLUSIONSOur results suggest that dimensional abnormalities in the activation of cognitive control regions were associated primarily with symptoms of depression (with or without controlling for anxious arousal). Furthermore, following treatment with CBT, activation of cognitive control regions was similarly increased in both MDD and PTSD. These results accord with the Research Domain Criteria conceptualization of mental disorders and implicate improved cognitive control activation as a transdiagnostic mechanism for CBT treatment outcome.
Pre-trained convolutional neural networks as feature extractors toward improved malaria parasite detection in thin blood smear images
Malaria is a blood disease caused by the Plasmodium parasites transmitted through the bite of female Anopheles mosquito. Microscopists commonly examine thick and thin blood smears to diagnose disease and compute parasitemia. However, their accuracy depends on smear quality and expertise in classifying and counting parasitized and uninfected cells. Such an examination could be arduous for large-scale diagnoses resulting in poor quality. State-of-the-art image-analysis based computer-aided diagnosis (CADx) methods using machine learning (ML) techniques, applied to microscopic images of the smears using hand-engineered features demand expertise in analyzing morphological, textural, and positional variations of the region of interest (ROI). In contrast, Convolutional Neural Networks (CNN), a class of deep learning (DL) models promise highly scalable and superior results with end-to-end feature extraction and classification. Automated malaria screening using DL techniques could, therefore, serve as an effective diagnostic aid. In this study, we evaluate the performance of pre-trained CNN based DL models as feature extractors toward classifying parasitized and uninfected cells to aid in improved disease screening. We experimentally determine the optimal model layers for feature extraction from the underlying data. Statistical validation of the results demonstrates the use of pre-trained CNNs as a promising tool for feature extraction for this purpose.
Spatial reversal learning defect coincides with hypersynchronous telencephalic BOLD functional connectivity in APPNL-F/NL-F knock-in mice
Amyloid pathology occurs early in Alzheimer’s disease (AD), and has therefore been the focus of numerous studies. Transgenic mouse models have been instrumental to study amyloidosis, but observations might have been confounded by APP-overexpression artifacts. The current study investigated early functional defects in an APP knock-in mouse model, which allows assessing the effects of pathological amyloid-beta (Aβ) without interference of APP-artifacts. Female APPNL/NL knock-in mice of 3 and 7 months old were compared to age-matched APPNL-F/NL-F mice with increased Aβ42/40 ratio and initial Aβ-plaque deposition around 6 months of age. Spatial learning was examined using a Morris water maze protocol consisting of acquisition and reversal trials interleaved with reference memory tests. Functional connectivity (FC) of brain networks was assessed using resting-state functional MRI (rsfMRI). The Morris water maze data revealed that 3 months old APPNL-F/NL-F mice were unable to reach the same reference memory proficiency as APPNL/NL mice after reversal training. This cognitive defect in 3-month-old APPNL-F/NL-F mice coincided with hypersynchronous FC of the hippocampal, cingulate, caudate-putamen, and default-mode-like networks. The occurrence of these defects in APPNL-F/NL-F mice demonstrates that cognitive flexibility and synchronicity of telencephalic activity are specifically altered by early Aβ pathology without changes in APP neurochemistry.
Nomograms to Predict Individual Prognosis of Patients with Primary Small Cell Carcinoma of the Bladder
Objectives: To develop reliable nomograms to estimate individualized overall survival (OS) and cancer specific survival (CSS) for patients with primary small cell carcinoma of the bladder (SCCB) and compare the predictive value with the AJCC stages.Patients and Methods: 582 eligible SCCB patients identified in the Surveillance, Epidemiology, and End Results (SEER) dataset were randomly divided into training (n=482) and validation (n=100) cohorts. Akaike information criterion was used to select the clinically important variables in multivariate Cox models when establishing nomograms. The performance of nomograms was bootstrapped validated internally and externally using the concordance index (C-index) with 95% confidence interval (95% CI) and calibration curves and was compared with that of the AJCC stages using C-index, Kaplan-Meier curves and decision curve analysis (DCA).Results: Two nomograms shared common indicators including age, tumor size, T stage, lymph node ratio, metastases, chemotherapy, radiation and radical cystectomy, while marriage and gender were only incorporated in the OS nomogram. The C-indices of nomograms for OS and CSS were 0.736 (95%CI 0.711-0.761) and 0.731(95%CI 0.704-0.758), respectively, indicating considerable predictive accuracy. Calibration curves showed consistency between the nomograms and the actual observation. The results remained reproducible when nomograms were applied to the validation cohort. Additionally, comparisons between C-indices, Kaplan-Meier curves and DCA proved that the nomograms obtained obvious superiority over the AJCC stages with wide practical threshold probabilities.Conclusions: We proposed the first two nomograms for individualized prediction of OS and CSS in SCCB patients with satisfactory predictive accuracy, good robustness and wide applicability.
Right Fronto-Subcortical White Matter Microstructure Predicts Cognitive Control Ability on the Go/No-go Task in a Community Sample
Go/no-go tasks are widely used to index cognitive control. This construct has been linked to white matter microstructure in a circuit connecting the right inferior frontal gyrus (IFG), subthalamic nucleus (STN), and pre-supplementary motor area. However, the specificity of this association has not been tested. A general factor of white matter has been identified that is related to processing speed. Given the strong processing speed component in successful performance on the go/no-go task, this general factor could contribute to task performance, but the general factor has often not been accounted for in past studies of cognitive control. Further, studies on cognitive control have generally employed small unrepresentative case-control designs. The present study examined the relationship between go/no-go performance and white matter microstructure in a large community sample of 378 subjects that included participants with a range of both clinical and subclinical nonpsychotic psychopathology. We found that white matter microstructure properties in the right IFG-STN tract significantly predicted task performance, and remained significant after controlling for dimensional psychopathology. The general factor of white matter only reached statistical significance when controlling for dimensional psychopathology. Although the IFG-STN and general factor tracts were highly correlated, when both were included in the model, only the IFG-STN remained a significant predictor of performance. Overall, these findings suggest that while a general factor of white matter can be identified in a young community sample, white matter microstructure properties in the right IFG-STN tract show a specific relationship to cognitive control. The findings highlight the importance of examining both specific and general correlates of cognition, especially in tasks with a speeded component.
L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib††Electronic supplementary information (ESI) available: pKa shift for Cys797; geometries of TSs identified with QM/MM calculations; analysis of the minimum free-energy path for Cys797 alkylation; analysis of MD replicas; convergence for US simulations; replica of simulation of Cys797 alkylation; conformational FESs obtained from each MD replica. See DOI: 10.1039/c7sc04761d
Impact of L718Q mutation on the inhibitory activity of osimertinib on EGFR revealed by free-energy simulations.
Tuning the redox non-innocence of a phenalenyl ligand toward efficient nickel-assisted catalytic hydrosilylation††Electronic supplementary information (ESI) available: Detailed experimental procedures, spectra (NMR and HRMS), CV, crystallographic details, and coordinates of the computed structures. CCDC 1518117. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc04687a
The hydrosilylation of olefins by a nickel(ii) catalyst assisted by a redox non-innocent phenalenyl (PLY) ligand is reported.
Proteome-wide analysis of cysteine oxidation reveals metabolic sensitivity to redox stress
Reactive oxygen species (ROS) are increasingly recognised as important signalling molecules through oxidation of protein cysteine residues. Comprehensive identification of redox-regulated proteins and pathways is crucial to understand ROS-mediated events. Here, we present stable isotope cysteine labelling with iodoacetamide (SICyLIA), a mass spectrometry-based workflow to assess proteome-scale cysteine oxidation. SICyLIA does not require enrichment steps and achieves unbiased proteome-wide sensitivity. Applying SICyLIA to diverse cellular models and primary tissues provides detailed insights into thiol oxidation proteomes. Our results demonstrate that acute and chronic oxidative stress causes oxidation of distinct metabolic proteins, indicating that cysteine oxidation plays a key role in the metabolic adaptation to redox stress. Analysis of mouse kidneys identifies oxidation of proteins circulating in biofluids, through which cellular redox stress can affect whole-body physiology. Obtaining accurate peptide oxidation profiles from complex organs using SICyLIA holds promise for future analysis of patient-derived samples to study human pathologies.
The PiGeOn project: protocol of a longitudinal study examining psychosocial and ethical issues and outcomes in germline genomic sequencing for cancer
BackgroundAdvances in genomics offer promise for earlier detection or prevention of cancer, by personalisation of medical care tailored to an individual’s genomic risk status. However genome sequencing can generate an unprecedented volume of results for the patient to process with potential implications for their families and reproductive choices. This paper describes a protocol for a study (PiGeOn) that aims to explore how patients and their blood relatives experience germline genomic sequencing, to help guide the appropriate future implementation of genome sequencing into routine clinical practice.MethodsWe have designed a mixed-methods, prospective, cohort sub-study of a germline genomic sequencing study that targets adults with cancer suggestive of a genetic aetiology. One thousand probands and 2000 of their blood relatives will undergo germline genomic sequencing as part of the parent study in Sydney, Australia between 2016 and 2020. Test results are expected within12–15 months of recruitment. For the PiGeOn sub-study, participants will be invited to complete surveys at baseline, three months and twelve months after baseline using self-administered questionnaires, to assess the experience of long waits for results (despite being informed that results may not be returned) and expectations of receiving them. Subsets of both probands and blood relatives will be purposively sampled and invited to participate in three semi-structured qualitative interviews (at baseline and each follow-up) to triangulate the data. Ethical themes identified in the data will be used to inform critical revisions of normative ethical concepts or frameworks.DiscussionThis will be one of the first studies internationally to follow the psychosocial impact on probands and their blood relatives who undergo germline genome sequencing, over time. Study results will inform ongoing ethical debates on issues such as informed consent for genomic sequencing, and informing participants and their relatives of specific results. The study will also provide important outcome data concerning the psychological impact of prolonged waiting for germline genomic sequencing. These data are needed to ensure that when germline genomic sequencing is introduced into standard clinical settings, ethical concepts are embedded, and patients and their relatives are adequately prepared and supported during and after the testing process.
In Vivo Multimodal Magnetic Resonance Imaging Changes After N-Methyl-d-Aspartate-Triggered Spasms in Infant Rats
ObjectiveDespite the serious neurodevelopmental sequelae of epileptic encephalopathy during infancy, the pathomechanisms involved remain unclear. To find potential biomarkers that can reflect the pathogenesis of epileptic encephalopathy, we explored the neurometabolic and microstructural sequelae after infantile spasms using a rat model of infantile spasms and in vivo magnetic resonance imaging techniques.MethodsRats prenatally exposed to betamethasone were subjected to three rounds of intraperitoneal N-methyl-d-aspartate (NMDA) triggering of spasms or received saline injections (controls) on postnatal days (P) 12, 13, and 15. Chemical exchange saturation transfer imaging of glutamate (GluCEST) were performed at P15 and 22 and diffusion tensor imaging and additional spectroscopy (1H-MRI/MRS) of the cingulate cortex were serially done at P16, 23, and 30 and analyzed. Pathological analysis and western blotting were performed with rats sacrificed on P35.ResultsWithin 24 h of the three rounds of NMDA-induced spasms, there was an acute increase in the GluCEST (%) in the cortex, hippocampus, and striatum. When focused on the cingulate cortex, mean diffusivity (MD) was significantly decreased during the acute period after multiple spasms with an increase in γ-aminobutyric acid (GABA), glutamate, and glutamine N-acetylaspartate-plus-N-acetylaspartylglutamate (tNAA), total choline, and total creatine. The juvenile rats also showed decreased MD on diffusion tensor imaging and significant decreases in taurine, tNAA, and macromolecules-plus-lipids in the cingulate cortex. Pathologically, there was a significant reduction in glial fibrillary acidic protein, myelin basic protein, and neuronal nuclei expression in the cingulate cortex of rats with NMDA-induced spasms.SignificanceThese neurometabolic and microstructural alterations after NMDA-triggered spasms might be potential imaging biomarkers of epileptic encephalopathy.
Brain mapping for long-term recovery of gait after supratentorial stroke
AbstractThe recovery of independent gait after stroke is a main goal of patients and understanding the relationship between brain lesions and the recovery of gait can help physicians set viable rehabilitation plans. Our study investigated the association between variables of gait parameters and brain lesions.Fifty poststroke patients with a mean age of 67.5 ± 1.3 years and an average duration after onset of 62.2 ± 7.9 months were included. Three-dimensional gait analysis and magnetic resonance imaging were conducted for all patients. Twelve quantified gait parameters of temporal-spatial, kinematic, and kinetic data were used. To correlate gait parameters with specific brain lesions, we used a voxel-based lesion symptom mapping analysis. Statistical significance was set to an uncorrected P value <.005 and cluster size >10 voxels.Based on the location of a brain lesion, the following results were obtained: The posterior limb of the internal capsule was significantly associated with gait speed and increased knee extension in the stance phase. The hippocampus and frontal lobe were significantly associated with cadence. The proximal corona radiata was significantly associated with stride length and affected the hip maximal extension angle in the stance phase. The paracentral lobule was significantly associated with the affected knee maximal flexion angle in the swing phase and with the affected ankle maximal dorsiflexion angle in the stance phase. The frontal lobe, thalamus, and the lentiform nucleus were associated with kinetic gait parameters.Cortical, proximal white matter, and learning-related and motor-related areas are mainly associated with one's walking ability after stroke.
Molecular responses to therapeutic proteasome inhibitors in multiple myeloma patients are donor-, cell type- and drug-dependent
Proteasome is central to proteostasis network functionality and its over-activation represents a hallmark of advanced tumors; thus, its selective inhibition provides a strategy for the development of novel antitumor therapies. In support, proteasome inhibitors, e.g. Bortezomib or Carfilzomib have demonstrated clinical efficacy against hematological cancers. Herein, we studied proteasome regulation in peripheral blood mononuclear cells and erythrocytes isolated from healthy donors or from Multiple Myeloma patients treated with Bortezomib or Carfilzomib. In healthy donors we found that peripheral blood mononuclear cells express higher, as compared to erythrocytes, basal proteasome activities, as well as that proteasome activities decline during aging. Studies in cells isolated from Multiple Myeloma patients treated with proteasome inhibitors revealed that in most (but, interestingly enough, not all) patients, proteasome activities decline in both cell types during therapy. In peripheral blood mononuclear cells, most proteostatic genes expression patterns showed a positive correlation during therapy indicating that proteostasis network modules likely respond to proteasome inhibition as a functional unit. Finally, the expression levels of antioxidant, chaperone and aggresomes removal/autophagy genes were found to inversely associate with patients’ survival. Our studies will support a more personalized therapeutic approach in hematological malignancies treated with proteasome inhibitors.
USP9X Limits Mitotic Checkpoint Complex Turnover to Strengthen the Spindle Assembly Checkpoint and Guard against Chromosomal Instability
SummaryFaithful chromosome segregation during mitosis depends on the spindle assembly checkpoint (SAC), which delays progression through mitosis until every chromosome has stably attached to spindle microtubules via the kinetochore. We show here that the deubiquitinase USP9X strengthens the SAC by antagonizing the turnover of the mitotic checkpoint complex produced at unattached kinetochores. USP9X thereby opposes activation of anaphase-promoting complex/cyclosome (APC/C) and specifically inhibits the mitotic degradation of SAC-controlled APC/C substrates. We demonstrate that depletion or loss of USP9X reduces the effectiveness of the SAC, elevates chromosome segregation defects, and enhances chromosomal instability (CIN). These findings provide a rationale to explain why loss of USP9X could be either pro- or anti-tumorigenic depending on the existing level of CIN.
Human papillomavirus genotype and viral load agreement between paired first-void urine and clinician-collected cervical samples
The performance and acceptability of first-void urine as specimen for the detection of HPV DNA in a Belgian referral population was evaluated using an optimized sample collection and processing protocol. One hundred ten first-void urine and cervical samples were collected from 25- to 64-year-old women who were referred for colposcopy (January–November 2016). Paired samples were analyzed by the Riatol qPCR HPV genotyping assay. Acceptability data were gathered through questionnaires (NCT02714127). A higher high-risk HPV DNA prevalence was observed in first-void urine (n = 76/110) compared to cervical samples (n = 73/110), with HPV31 and HPV16/31 being most prevalent correspondingly. For both any and high-risk HPV DNA, good agreement was observed between paired samples (Cohen’s Kappa of 0.660 (95% CI: 0.486–0.833) and 0.688 (95% CI: 0.542–0.835), respectively). In addition, significant positive correlations in HPV copies (per microliter of DNA extract) between paired samples were observed for HPV16 (rs = 0.670; FDR (false discovery rate)-adjusted p = 0.006), HPV18 (rs = 0.893; FDR-adjusted p = 0.031), HPV31 (rs = 0.527; FDR-adjusted p = 0.031), HPV53 (rs = 0.691; FDR-adjusted p = 0.017), and HPV68 (rs = 0.569; FDR-adjusted p = 0.031). First-void urine sampling using a first-void urine collection device was preferred over a clinician-collected cervical sample. And mostly, first-void urine sampling at home was favored over collection at the clinic or the general practitioner’s office. First-void urine sampling is a highly preferred, non-invasive method that ensures good agreement in HPV DNA (copies) with reference cervical samples. It is particularly interesting as a screening technique to reach non-participants, and its clinical performance should be further evaluated.Electronic supplementary materialThe online version of this article (10.1007/s10096-017-3179-1) contains supplementary material, which is available to authorized users.
Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas
Species and populations are disappearing at an alarming rate as a direct result of human activities. Loss of genetic diversity associated with population decline directly impacts species’ long-term survival. Therefore, preserving genetic diversity is of considerable conservation importance. However, to assist in conservation efforts, it is important to understand how genetic diversity is spatially distributed and how it changes due to anthropogenic pressures. In this study, we use historical museum and modern faecal samples of two critically endangered eastern gorilla taxa, Grauer’s (Gorilla beringei graueri) and mountain gorillas (Gorilla beringei beringei), to directly infer temporal changes in genetic diversity within the last century. Using over 100 complete mitochondrial genomes, we observe a significant decline in haplotype and nucleotide diversity in Grauer’s gorillas. By including historical samples from now extinct populations we show that this decline can be attributed to the loss of peripheral populations rather than a decrease in genetic diversity within the core range of the species. By directly quantifying genetic changes in the recent past, our study shows that human activities have severely impacted eastern gorilla genetic diversity within only four to five generations. This rapid loss calls for dedicated conservation actions, which should include preservation of the remaining peripheral populations.
Contrasting patterns of Andean diversification among three diverse clades of Neotropical clearwing butterflies
AbstractThe Neotropical region is the most biodiverse on Earth, in a large part due to the highly diverse tropical Andean biota. The Andes are a potentially important driver of diversification within the mountains and for neighboring regions. We compared the role of the Andes in diversification among three subtribes of Ithomiini butterflies endemic to the Neotropics, Dircennina, Oleriina, and Godyridina. The diversification patterns of Godyridina have been studied previously. Here, we generate the first time‐calibrated phylogeny for the largest ithomiine subtribe, Dircennina, and we reanalyze a published phylogeny of Oleriina to test different biogeographic scenarios involving the Andes within an identical framework. We found common diversification patterns across the three subtribes, as well as major differences. In Dircennina and Oleriina, our results reveal a congruent pattern of diversification related to the Andes with an Andean origin, which contrasts with the Amazonian origin and multiple Andean colonizations of Godyridina. In each of the three subtribes, a clade diversified in the Northern Andes at a faster rate. Diversification within Amazonia occurred in Oleriina and Godyridina, while virtually no speciation occurred in Dircennina in this region. Dircennina was therefore characterized by higher diversification rates within the Andes compared to non‐Andean regions, while in Oleriina and Godyridina, we found no difference between these regions. Our results and discussion highlight the importance of comparative approaches in biogeographic studies.
Vascular reactivity in small cerebral perforating arteries with 7 T phase contrast MRI – A proof of concept study
Existing cerebrovascular reactivity (CVR) techniques assess flow reactivity in either the largest cerebral vessels or at the level of the parenchyma. We examined the ability of 2D phase contrast MRI at 7 T to measure CVR in small cerebral perforating arteries.Blood flow velocity in perforators was measured in 10 healthy volunteers (mean age 26 years) using a 7 T MR scanner, using phase contrast acquisitions in the semioval center (CSO), the basal ganglia (BG) and the middle cerebral artery (MCA). Changes in flow velocity in response to a hypercapnic breathing challenge were assessed, and expressed as the percentual increase of flow velocity as a function of the increase in end tidal partial pressure of CO2.The hypercapnic challenge increased (fit ± standard error) flow velocity by 0.7 ± 0.3%/mmHg in the CSO (P < 0.01). Moreover, the number of detected perforators (mean [range]) increased from 63 [27–88] to 108 [61–178] (P < 0.001). In the BG, the hypercapnic challenge increased flow velocity by 1.6 ± 0.5%/mmHg (P < 0.001), and the number of detected perforators increased from 48 [24–66] to 63 [32–91] (P < 0.01). The flow in the MCA increased by 5.2 ± 1.4%/mmHg (P < 0.01).Small vessel specific reactivity can now be measured in perforators of the CSO and BG, using 2D phase contrast at 7 T.
Positive selection drives the evolution of endocrine regulatory bone morphogenetic protein system in mammals
The rapid evolution of reproductive proteins might be driven by positive Darwinian selection. The bone morphogenetic protein family is the largest within the transforming growth factor (TGF) superfamily. A little have been known about the molecular evolution of bone morphogenetic proteins exhibiting potential role in mammalian reproduction. In this study we investigated mammalian bone morphogenetic proteins using maximum likelihood approaches of codon substitutions to identify positive Darwinian selection in various species. The proportion of positively selected sites was tested by different likelihood models for individual codon, and M8 were found to be the best model. The percentage of positively elected sites under M8 are 2.20% with ω = 1.089 for BMP2, 1.6% with ω = 1.61 for BMP 4 0.53% for BMP15 with ω = 1.56 and 0.78% for GDF9 with ω = 1.93. The percentage of estimated selection sites under M8 is strong statistical confirmation that divergence of bone morphogenetic proteins is driven by Darwinian selection. For the proteins, model M8 was found significant for all proteins with ω > 1. To further test positive selection on particular amino acids, the evolutionary conservation of amino acid were measured based on phylogenetic linkage among sequences. For exploring the impact of these somatic substitution mutations in the selection region on human cancer, we identified one pathogenic mutation in human BMP4 and one in BMP15, possibly causing prostate cancer and six neutral mutations in BMPs. The comprehensive map of selection results allows the researchers to perform systematic approaches to detect the evolutionary footprints of selection on specific gene in specific species.
Structural basis for the activation of acid ceramidase
Acid ceramidase (aCDase, ASAH1) hydrolyzes lysosomal membrane ceramide into sphingosine, the backbone of all sphingolipids, to regulate many cellular processes. Abnormal function of aCDase leads to Farber disease, spinal muscular atrophy with progressive myoclonic epilepsy, and is associated with Alzheimer’s, diabetes, and cancer. Here, we present crystal structures of mammalian aCDases in both proenzyme and autocleaved forms. In the proenzyme, the catalytic center is buried and protected from solvent. Autocleavage triggers a conformational change exposing a hydrophobic channel leading to the active site. Substrate modeling suggests distinct catalytic mechanisms for substrate hydrolysis versus autocleavage. A hydrophobic surface surrounding the substrate binding channel appears to be a site of membrane attachment where the enzyme accepts substrates facilitated by the accessory protein, saposin-D. Structural mapping of disease mutations reveals that most would destabilize the protein fold. These results will inform the rational design of aCDase inhibitors and recombinant aCDase for disease therapeutics.
Trypanosomal mitochondrial intermediate peptidase does not behave as a classical mitochondrial processing peptidase
Upon their translocation into the mitochondrial matrix, the N-terminal pre-sequence of nuclear-encoded proteins undergoes cleavage by mitochondrial processing peptidases. Some proteins require more than a single processing step, which involves several peptidases. Down-regulation of the putative Trypanosoma brucei mitochondrial intermediate peptidase (MIP) homolog by RNAi renders the cells unable to grow after 48 hours of induction. Ablation of MIP results in the accumulation of the precursor of the trypanosomatid-specific trCOIV protein, the largest nuclear-encoded subunit of the cytochrome c oxidase complex in this flagellate. However, the trCOIV precursor of the same size accumulates also in trypanosomes in which either alpha or beta subunits of the mitochondrial processing peptidase (MPP) have been depleted. Using a chimeric protein that consists of the N-terminal sequence of a putative subunit of respiratory complex I fused to a yellow fluorescent protein, we assessed the accumulation of the precursor protein in trypanosomes, in which RNAi was induced against the alpha or beta subunits of MPP or MIP. The observed accumulation of precursors indicates MIP depletion affects the activity of the cannonical MPP, or at least one of its subunits.
Optically-controlled bacterial metabolite for cancer therapy
Bacteria preferentially accumulating in tumor microenvironments can be utilized as natural vehicles for tumor targeting. However, neither current chemical nor genetic approaches alone can fully satisfy the requirements on both stability and high efficiency. Here, we propose a strategy of “charging” bacteria with a nano-photocatalyst to strengthen their metabolic activities. Carbon nitride (C3N4) is combined with Escherichia coli (E. coli) carrying nitric oxide (NO) generation enzymes for photo-controlled bacterial metabolite therapy (PMT). Under light irradiation, photoelectrons produced by C3N4 can be transferred to E. coli to promote the enzymatic reduction of endogenous NO3– to cytotoxic NO with a 37-fold increase. In a mouse model, C3N4 loaded bacteria are perfectly accumulated throughout the tumor and the PMT treatment results in around 80% inhibition of tumor growth. Thus, synthetic materials-remodeled microorganism may be used to regulate focal microenvironments and increase therapeutic efficiency.
Quantifying the impact on navigation performance in visually impaired: Auditory information loss versus information gain enabled through electronic travel aids
This study’s purpose was to analyze and quantify the impact of auditory information loss versus information gain provided by electronic travel aids (ETAs) on navigation performance in people with low vision. Navigation performance of ten subjects (age: 54.9±11.2 years) with visual acuities >1.0 LogMAR was assessed via the Graz Mobility Test (GMT). Subjects passed through a maze in three different modalities: ‘Normal’ with visual and auditory information available, ‘Auditory Information Loss’ with artificially reduced hearing (leaving only visual information), and ‘ETA’ with a vibrating ETA based on ultrasonic waves, thereby facilitating visual, auditory, and tactile information. Main performance measures comprised passage time and number of contacts. Additionally, head tracking was used to relate head movements to motion direction. When comparing ‘Auditory Information Loss’ to ‘Normal’, subjects needed significantly more time (p<0.001), made more contacts (p<0.001), had higher relative viewing angles (p = 0.002), and a higher percentage of orientation losses (p = 0.011). The only significant difference when comparing ‘ETA’ to ‘Normal’ was a reduced number of contacts (p<0.001). Our study provides objective, quantifiable measures of the impact of reduced hearing on the navigation performance in low vision subjects. Significant effects of ‘Auditory Information Loss’ were found for all measures; for example, passage time increased by 17.4%. These findings show that low vision subjects rely on auditory information for navigation. In contrast, the impact of the ETA was not significant but further analysis of head movements revealed two different coping strategies: half of the subjects used the ETA to increase speed, whereas the other half aimed at avoiding contacts.
High throughput evaluation of macrocyclization strategies for conformer stabilization
While macrocyclization of a linear compound to stabilize a known bioactive conformation can be a useful strategy to increase binding potency, the difficulty of macrocycle synthesis can limit the throughput of such strategies. Thus computational techniques may offer the higher throughput required to screen large numbers of compounds. Here we introduce a method for evaluating the propensity of a macrocyclic compound to adopt a conformation similar that of a known active linear compound in the binding site. This method can be used as a fast screening tool for prioritizing macrocycles by leveraging the assumption that the propensity for the known bioactive substructural conformation relates to the affinity. While this method cannot to identify new interactions not present in the known linear compound, it could quickly differentiate compounds where the three dimensional geometries imposed by the macrocyclization prevent adoption of conformations with the same contacts as the linear compound in their conserved region. Here we report the implementation of this method using an RMSD-based structural descriptor and a Boltzmann-weighted propensity calculation and apply it retrospectively to three macrocycle linker optimization design projects. We found the method performs well in terms of prioritizing more potent compounds.
Rapid detection of Puccinia triticina causing leaf rust of wheat by PCR and loop mediated isothermal amplification
Leaf rust of wheat caused by Puccinia triticina has significant impact on wheat production worldwide. Effective and quick detection methodologies are required to mitigate yield loss and time constraints associated with monitoring and management of leaf rust of wheat. In the present study, detection of P. triticina has been simplified by developing a rapid, reliable, efficient and visual colorimetric method i.e., loop mediated isothermal amplification of DNA (LAMP). Based on in silico analysis of P. triticina genome, PTS68, a simple sequence repeat was found highly specific to leaf rust fungus. A marker (PtRA68) was developed and its specificity was validated through PCR technique which gave a unique and sharp band of 919 bp in P. triticina pathotypes only. A novel gene amplification method LAMP which enables visual detection of pathogen by naked eye was developed for leaf rust pathogen. A set of six primers was designed from specific region of P. triticina and conditions were optimised to complete the observation process in 60 minutes at 65o C. The assay developed in the study could detect presence of P. triticina on wheat at 24 hpi (pre-symptomatic stage) which was much earlier than PCR without requiring thermal cycler. Sensitivity of LAMP assay developed in the study was 100 fg which was more sensitive than conventional PCR (50 pg) and equivalent to qPCR (100 fg). The protocol developed in the study was utilized for detection of leaf rust infected samples collected from different wheat fields. LAMP based colorimetric detection assay showed sky blue color in positive reaction and violet color in negative reaction after addition of 120 μM hydroxyl napthol blue (HNB) solution to reaction mixture. Similarly, 0.6 mg Ethidium bromide/ml was added to LAMP products, placed on transilluminator to witness full brightness in positive reaction and no such brightness could be seen in negative reaction mixture. Further, LAMP products spread in a ladder like banding pattern in gel electrophoresis. Our assay is significantly faster than the conventional methods used in the identification of P. triticina. The assay developed in the study shall be very much useful in the development of diagnostic kit for monitoring disease, creation of prediction model and efficient management of disease.
Influence of region-of-interest designs on quantitative measurement of multimodal imaging of MR non-enhancing gliomas
A number of studies have revealed the usefulness of multimodal imaging in gliomas. Although the results have been heavily affected by the method used for region of interest (ROI) design, the most discriminatory method for setting the ROI remains unclear. The aim of the present study was to determine the most suitable ROI design for 18F-fluorodeoxyglucose (FDG) and 11C-methionine (MET) positron emission tomography (PET), apparent diffusion coefficient (ADC), and fractional anisotropy (FA) obtained by diffusion tensor imaging (DTI) from the viewpoint of grades of non-enhancing gliomas. A total of 31 consecutive patients with newly diagnosed, histologically confirmed magnetic resonance (MR) non-enhancing gliomas who underwent FDG-PET, MET-PET and DTI were retrospectively investigated. Quantitative measurements were performed using four different ROIs; hotspot/tumor center and whole tumor, constructed in either two-dimensional (2D) or three-dimensional (3D). Histopathological grading of the tumor was considered as empirical truth and the quantitative measurements obtained from each ROI was correlated with the grade of the tumor. The most discriminating ROI for non-enhancing glioma grading was different according to the different imaging modalities. 2D-hotspot/center ROI was most discriminating for FDG-PET (P=0.087), ADC map (P=0.0083), and FA map (P=0.25), whereas 3D-whole tumor ROI was best for MET-PET (P=0.0050). In the majority of scenarios, 2D-ROIs performed better than 3D-ROIs. Results from the image analysis using FDG-PET, MET-PET, ADC and FA may be affected by ROI design and the most discriminating ROI for non-enhancing glioma grading was different according to the imaging modality.
Comparative analyses and structural insights of the novel cytochrome P450 fusion protein family CYP5619 in Oomycetes
Phylogenetic and structural analysis of P450 proteins fused to peroxidase/dioxygenase has not been reported yet. We present phylogenetic and in silico structural analysis of the novel P450 fusion family CYP5619 from the deadliest fish pathogenic oomycete, Saprolegnia diclina. Data-mining and annotation of CYP5619 members revealed their unique presence in oomycetes. CYP5619 members have the highest number of conserved amino acids among eukaryotic P450s. The highest number of conserved amino acids (78%) occurred in the peroxidase/dioxygenase domain compared to the P450 domain (22%). In silico structural analysis using a high-quality CYP5619A1 model revealed that CYP5619A1 has characteristic P450 structural motifs including EXXR and CXG. However, the heme-binding domain (CXG) in CYP5619 members was found to be highly degenerated. The in silico substrate binding pattern revealed that CYP5619A1 have a high affinity to medium chain fatty acids. Interestingly, the controlling agent of S. diclina malachite green was predicted to have the highest binding affinity, along with linoleic acid. However, unlike fatty acids, none of the active site amino acids formed hydrogen bonds with malachite green. The study’s results will pave the way for assessing CYP5619A1’s role in S. diclina physiology, including the nature of malachite green binding.
The Comorbidity Between Internet Gaming Disorder and Depression: Interrelationship and Neural Mechanisms
Internet gaming disorder (IGD) is characterized by cognitive and emotional deficits. Previous studies have reported the co-occurrence of IGD and depression. However, extant brain imaging research has largely focused on cognitive deficits in IGD. Few studies have addressed the comorbidity between IGD and depression symptoms and underlying neural mechanisms. Here, we systematically investigated this issue by combining a longitudinal survey study, a cross-sectional resting-state functional connectivity (rsFC) study and an intervention study. Autoregressive cross-lagged modeling on a longitudinal dataset of college students showed that IGD severity and depression are reciprocally predictive. At the neural level, individuals with IGD exhibited enhanced rsFC between the left amygdala and right dorsolateral prefrontal cortex (DLPFC), inferior frontal and precentral gyrus, compared with control participants, and the amygdala-frontoparietal connectivity at the baseline negatively predicted reduction in depression symptoms following a psychotherapy intervention. Further, following the intervention, individuals with IGD showed decreased connectivity between the left amygdala and left middle frontal and precentral gyrus, as compared with the non-intervention group. These findings together suggest that IGD may be closely associated with depression; aberrant rsFC between emotion and executive control networks may underlie depression and represent a therapeutic target in individuals with IGD.Registry name: The behavioral and brain mechanism of IGD;URL: https://www.clinicaltrials.gov/ct2/show/NCT02550405;Registration number: NCT02550405.